Superposition Approximation Research Articles

Tracing the classical molecular nature of entropy generation

The second law of thermodynamics and the concept of positive entropy generation are analyzed following classical statistical mechanics methods. Previously, using the generalized Boltzmann–Gibbs entropy and its associated general entropy conservation relation, positive entropy generation expressions were obtained in agreement with phenomenological results and the work of Boltzmann and Gibbs. In this study, using the general approach, we formally and explicitly trace the specific entropy generation expressions to truncations in the full N-body description of the entropy state to a lower s-body description. Using higher-order superposition approximations, it is formally shown that the generalized Boltzmann–Gibbs entropy in the s-order state is always less than the corresponding Boltzmann–Gibbs entropy in the lower (s − 1)-order state. Using the general form of the entropy conservation equation, entropy generation is shown to be a required compensatory effect to ensure that all physical variables and physical processes associated with heat, work, temperature, etc., are independent of the particular entropy definition state.

Effect of the nature of the solid substrate on spatially heterogeneous activated dynamics in glass forming supported films.

We extend the force-level elastically collective nonlinear Langevin equation theory to treat the spatial gradients of the alpha relaxation time and glass transition temperature, and the corresponding film-averaged quantities, to the geometrically asymmetric case of finite thickness supported films with variable fluid-substrate coupling. The latter typically nonuniversally slows down motion near the solid-liquid interface as modeled via modification of the surface dynamic free energy caging constraints that are spatially transferred into the film and which compete with the accelerated relaxation gradient induced by the vapor interface. Quantitative applications to the foundational hard sphere fluid and a polymer melt are presented. The strength of the effective fluid-substrate coupling has very large consequences for the dynamical gradients and film-averaged quantities in a film thickness and thermodynamic state dependent manner. The interference of the dynamical gradients of opposite nature emanating from the vapor and solid interfaces is determined, including the conditions for the disappearance of a bulk-like region in the film center. The relative importance of surface-induced modification of local caging vs the generic truncation of the long range collective elastic component of the activation barrier is studied. The conditions for the accuracy and failure of a simple superposition approximation for dynamical gradients in thin films are also determined. The emergence of near substrate dead layers, large gradient effects on film-averaged response functions, and a weak non-monotonic evolution of dynamic gradients in thick and cold films are briefly discussed. The connection of our theoretical results to simulations and experiments is briefly discussed, as is the extension to treat more complex glass-forming systems under nanoconfinement.

Hydrogen bond network structures of protonated 2,2,2-trifluoroethanol/ethanol mixed clusters probed by infrared spectroscopy combined with a deep-learning structure sampling approach: the origin of the linear type network preference in protonated fluoroalcohol clusters.

While preferential hydrogen bond network structures of cold protonated alcohol clusters H+(ROH)n are generally switched from a linear type to a cyclic one at n = 4-5, those of protonated 2,2,2-trifluoroethanol (TFE) clusters maintain linear type structures at least in the size range of n = 3-7. To explore the origin of the strong linear type network preference of H+(TFE)n, infrared spectra of protonated mixed clusters H+(TFE)m(ethanol)n (m + n = 5) were measured. An efficient structure sampling technique using parallelized basin-hopping algorithms and deep-learning neural network potentials is developed to search for essential isomers of the mixed clusters. Vibrational simulations based on the harmonic superposition approximation were compared with the observed spectra to identify the major isomer component at each mixing ratio. It was found that the formation of the cyclic structure occurs only in n ≥ 3 of the mixed clusters, in which the proton solvating sites and the double acceptor site are occupied by ethanol. The crucial role of the stability of the double acceptor site in the cyclic structure formation is discussed.

Tetrahedral Clusters Stabilized by Alloying.

A family of nanoclusters of tetrahedral symmetry is proposed. These clusters consist of symmetrically truncated tetrahedra with additional hexagonal islands on the four facets of the starting tetrahedron. The islands are placed in stacking fault positions. The geometric magic numbers of these clusters are derived. Global optimization searches within an atomistic potential model of Pt-Pd show that the tetrahedral structures can be stabilized for intermediate compositions of these nanoalloys, even when they are not the most stable structures of the elemental clusters. These results are also confirmed by density functional theory calculations for the magic sizes 59, 100, and 180. A thermodynamic analysis by the harmonic superposition approximation shows that Pt-Pd tetrahedral nanoalloys can be stable even above room temperature.

Computing Acceleration to Genome-Wide Association Study Based on CPU/FPGA Heterogeneous System

Genome Wide Association Study (GWAS) reveals the influence of single nucleotide polymorphisms (SNP) and other genetic markers on the complex genetic disease traits, making a significant contribution to the prevention and treatment of genetic diseases. Since GWAS needs to calculate large numbers of pairwise tests, it is highly time-consuming and this limits its widespread promotion in many medical applications. To solve the above problem, many studies deploy GWAS on the CPU/GPU platform. By taking advantages of GPUs' high parallelism, the completion time of GWAS can be significantly decreased. However, GPUs have high energy consumption, which increases GWAS's operating cost. Considering FPGA has low power, high parallelism and programmability, this article aims to use FPGA to design a hardware accelerator dedicated to GWAS for the purpose of optimizing both completion time and energy cost of GWAS. First, the CPU/FPGA heterogenous computing system is built, and the computationally-intensive GWAS tasks such as the contingency table creation (CTC) and Kirkwood Superposition Approximation (KSA) screening are offloaded to run on FPGA. Then, a specific FPGA architectures dedicated to CTC and KSA tasks of GWAS are implemented by using a set of architectural design technologies such as hardware and software co-optimization, systolic array, loop unrolling, pipeline and parallelism. To evaluate the performance of FPGA, we compare its completion time, energy cost and performance per Watt with those of CPU and GPU. The results show the FPGA and GPU can respectively achieve 105--fold and 148--fold speedup compared with CPU. Although FPGA's computing performance is a bit lower than that of GPU, it has higher energy efficiency and its performance per Watt is 1.4 times that of GPU.

Structural transformations in Cu, Ag, and Au metal nanoclusters.

Finite-temperature structures of Cu, Ag, and Au metal nanoclusters are calculated in the entire temperature range from 0K to melting using a computational methodology that we proposed recently [M. Settem et al., Nanoscale 14, 939 (2022)]. In this method, Harmonic Superposition Approximation (HSA) and Parallel Tempering Molecular Dynamics (PTMD) are combined in a complementary manner. HSA is accurate at low temperatures and fails at higher temperatures. PTMD, on the other hand, effectively samples the high temperature region and melts. This method is used to study the size- and system-dependent competition between various structural motifs of Cu, Ag, and Au nanoclusters in the size range 1-2nm. Results show that there are mainly three types of structural changes in metal nanoclusters, depending on whether a solid-solid transformation occurs. In the first type, the global minimum is the dominant motif in the entire temperature range. In contrast, when a solid-solid transformation occurs, the global minimum transforms either completely to a different motif or partially, resulting in the co-existence of multiple motifs. Finally, nanocluster structures are analyzed to highlight the system-specific differences across the three metals.

Modelling and model validation of particle stability and detachment from the particle-laden surface

Particle-bubble aggregates in flotation are characteristic of particle-laden bubbles and surfaces, but the available theories focus on the stability and detachment of single particle that resides lonely at the free surface. There is no modelling attempt to quantify the particle stability and detachment from the laden surfaces that can be relevant to flotation. Here, we developed a model that considers the particle tenacity (maximum adhesion force) at the particle-laden surface by solving the Young-Laplace equation (YLE) using the superposition approximation method. The vertical position of the target particle was calculated by considering the additive effect on the position by other nearby particles at the laden surface, based on the linearised YLE. Using the numerical results, a semi-empirical model for the particle tenacity was developed for engineering calculation exercises and assessed against the data of film flotation experiments. Application of the model to the case of changing contact angle was also established. The tenacity of particles at the laden surface was shown to be higher than at the free surface due to the lateral capillary attraction. This is the first model to quantify the particle stability and detachment from the particle-laden surface that can be useful for flotation.

Collision-induced three-body polarizability of helium.

We present the first-principles determination of the three-body polarizability and the third dielectric virial coefficient of helium. Coupled-cluster and full configuration interaction methods were used to perform electronic structure calculations. The mean absolute relative uncertainty of the trace of the polarizability tensor, resulting from the incompleteness of the orbital basis set, was found to be 4.7%. Additional uncertainty due to the approximate treatment of triple and the neglect of higher excitations was estimated at 5.7%. An analytic function was developed to describe the short-range behavior of the polarizability and its asymptotics in all fragmentation channels. We calculated the third dielectric virial coefficient and its uncertainty using the classical and semiclassical Feynman-Hibbs approaches. The results of our calculations were compared with experimental data and with recent Path-Integral Monte Carlo (PIMC) calculations [Garberoglio et al., J. Chem. Phys. 155, 234103 (2021)] employing the so-called superposition approximation of the three-body polarizability. For temperatures above 200K, we observed a significant discrepancy between the classical results obtained using superposition approximation and the ab initio computed polarizability. For temperatures from 10K up to 200K, the differences between PIMC and semiclassical calculations are several times smaller than the uncertainties of our results. Except at low temperatures, our results agree very well with the available experimental data but have much smaller uncertainties. The data reported in this work eliminate the main accuracy bottleneck in the optical pressure standard [Gaiser et al., Ann. Phys. 534, 2200336 (2022)] and facilitate further progress in the field of quantum metrology.

Analysis of the finite-size effect of the long-range Ising model under Glauber dynamics

We considered a long-range Ising model under Glauber dynamics and calculated the difference from the mean-field approximation in a finite-size system using perturbation theory. To deal with the Bogoliubov–Born–Green–Kirkwood–Yvon hierarchy, we assumed that certain types of extensive properties have a Gaussian distribution, which turned out to be equivalent to the Kirkwood superposition approximation within the range of first-order perturbation. After several calculations, ordinary differential equations that describe the time development of a two-body correlation were derived. This discussion is the generalization of our previous study which developed a similar consideration on the infinite-range Ising model. The results of the calculation fit those of the numerical simulations for the case in which the decay of the interaction was sufficiently slow; however, they exhibited different behaviors when the decay became rapid.

A pairwise hydrodynamic theory for flow-induced particle transport in shear and pressure-driven flows

An exact pairwise hydrodynamic theory is developed for the flow-induced spatial distribution of particles in dilute polydisperse suspensions undergoing two-dimensional unidirectional flows, including shear and planar Poiseuille flows. Coupled diffusive fluxes and a drift velocity are extracted from a Boltzmann-like master equation. A boundary layer is predicted in regions where the shear rate vanishes with thickness set by the radii of the upstream collision cross-sections for pair interactions. An analysis of this region yields linearly vanishing drift velocities and non-vanishing diffusivities where the shear rate vanishes, thus circumventing the source of the singular particle distribution predicted by the usual models. Outside of the boundary layer, a power-law particle distribution is predicted with exponent equal to minus half the exponent of the local shear rate. Trajectories for particles with symmetry-breaking contact interactions (e.g. rough particles, permeable particles, emulsion drops) are analytically integrated to yield particle displacements given by quadratures of hard-sphere (or spherical drop) mobility functions. Using this analysis, stationary particle distributions are obtained for suspensions in Poiseuille flow. The scale for the particle distribution in monodisperse suspensions is set by the collision cross-section of the particles but its shape is almost universal. Results for polydisperse suspensions show size segregation in the central boundary layer with enrichment of smaller particles. Particle densities at the centreline scale approximately with the inverse square root of particle size. A superposition approximation reliably predicts the exact results over a broad range of parameters. The predictions agree with experiments in suspensions up to approximately 20 % volume fraction without fitting parameters.

Choice of DLVO approximation method for quantifying the affinity between latex particles and membranes

The Derjaguin-Landau-Verwey-Overbeek (DLVO) model, as well as the extended model (XDLVO), is popularly employed to quantify the interfacial interactions underlying membrane fouling. However, disagreements between membrane fouling extent and the interaction energies derived from DLVO or XDLVO models have been reported, which suggests gaps in the understanding. This study demonstrates that the DLVO approximation methods for predicting the interfacial foulant-membrane interaction are sensitive to the boundary condition assumptions (e.g., constant charge versus constant potential). In particular, while both the Poisson-Boltzmann (P–B) and linear superposition approximation (LSA) equations can quantify the electrostatics (EL) interaction energy component, the former assumes constant potential, while the latter additionally considers constant charge scenarios. The relative accuracy of these two equations were evaluated here. For dead-end filtration tests, flux decline trends, OCT analysis results and fouling model parameters were obtained. Regarding fouling of pristine PCTE membrane by latex particles of opposite charge signs, both the P–B and LSA equations contribute to predict relative fouling extents correctly. However, for the case of the BPEI-coated membrane, the P–B equation failed whereas the LSA equation gave good agreements. For cross-flow filtration tests in organic solvents, LSA also out-performed the P–B equation in providing more accurate predictions of membrane fouling. The results here highlight the shortcomings in the commonly used P–B equation and are expected to be potentially valuable in the development of better approximations for quantifying interfacial interaction energies.

Controlled gel expansion through colloid oscillation.

We model the behavior of a single colloid embedded in a cross-linked polymer gel, immersed in a viscous background fluid. External fields actuate the particle into a periodic motion, which deforms the embedding matrix and creates a local microcavity, containing the particle and any free volume created by its motion. This cavity exists only as long as the particle is actuated and, when present, reduces the local density of the material, leading to swelling. We show that the model exhibits rich resonance features, but is overall characterized by clear scaling laws at low and high driving frequencies, and a pronounced resonance at intermediate frequencies. Our model predictions suggest that both the magnitude and position of the resonance can be varied by varying the material's elastic modulus or cross-linking density, whereas the local viscosity primarily has a dampening effect. Our work implies appreciable free-volume generation is possible by dispersing a collection of colloids in the medium, even at the level of a simple superposition approximation.

Range of applicability of real mode superposition approximation method for seismic response calculation of non-classically damped industrial buildings

Range of applicability of real mode superposition approximation method for seismic response calculation of non-classically damped industrial buildings

Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt\u2013water mixtures

Hydration thermodynamics play a fundamental role in fields ranging from the pharmaceutical industry to environmental research. Numerous methods exist to predict solvation thermodynamics of compounds ranging from small molecules to large biomolecules. Arguably the most precise methods are those based on molecular dynamics (MD) simulations in explicit solvent. One theory that has seen increased use is inhomogeneous solvation theory (IST). However, while many applications require accurate description of salt–water mixtures, no implementation of IST is currently able to estimate solvation properties involving more than one solvent species. Here, we present an extension to grid inhomogeneous solvation theory (GIST) that can take salt contributions into account. At the example of carbazole in 1 M NaCl solution, we compute the solvation energy as well as first and second order entropies. While the effect of the first order ion entropy is small, both the water–water and water–ion entropies contribute strongly. We show that the water–ion entropies are efficiently approximated using the Kirkwood superposition approximation. However, this approach cannot be applied to the water–water entropy. Furthermore, we test the quantitative validity of our method by computing salting-out coefficients and comparing them to experimental data. We find a good correlation to experimental salting-out constants, while the absolute values are overpredicted due to the approximate second order entropy. Since ions are frequently used in MD, either to neutralize the system or as a part of the investigated process, our method greatly extends the applicability of GIST. The use-cases range from biopharmaceuticals, where many assays require high salt concentrations, to environmental research, where solubility in sea water is important to model the fate of organic substances.

Electrostatic interaction between two spheroidal particles at large separations

Asymptotic expressions for the electrostatic interaction energy between two weakly charged spheroidal particles (prolate and oblate) with uniform surface potential or surface charge density at large separations in an electrolyte solution are derived on the basis of the linear superposition approximation. The electrostatic interaction between two spheroids is found to be the screened Coulomb interaction between two hypothetical point particles with orientation-dependent charges. Explicit interaction energy equations, which are expressed in terms of spheroidal wave functions, are given for four particular configurations of two similar spheroids, that is, side-to-side prolates, end-to-end prolates, side-to-side oblates, and end-to-end oblates. Comparison is also made with results obtained using Derjaguin’s approximation. Electrostatic interaction between two spheroids • Asymptotic expressions for the electrostatic interaction energy between two spheroidal particles are derived. • Constant surface potential and charge density cases are considered. • Side-to-side prolates, end-to-end prolates, side-to-side oblates, and end-to-end oblates are considered.

Analytical Modeling of Triple-Material Trigate Junctionless Tunnel Field Effect Transistor

An analytical two-dimensional (2D) model is developed to obtain expressions for various parameters of triple-material trigate junctionless tunnel field-effect transistors (TMTG-JTFETs). The 2D Poisson’s equation uses the superposition approximation method to calculate the sum of potentials arising from different point charges. The electric field distribution in the channel is obtained from the gradient of the electric potential. The drain current of the device is calculated using the Kane’s model in the presence of an electric field and a band structure. The TMTG-JTFET, with a channel length of 40nm, exhibits significant electrical characteristics with very low off-current (Ioff) and high on-current compared to a dual-material double-gate TFET. To validate the model, analytical results are confirmed via comparison with technology computer-aided design simulation results.

Nature of dynamic gradients, glass formation, and collective effects in ultrathin freestanding films

Molecular, polymeric, colloidal, and other classes of liquids can exhibit very large, spatially heterogeneous alterations of their dynamics and glass transition temperature when confined to nanoscale domains. Considerable progress has been made in understanding the related problem of near-interface relaxation and diffusion in thick films. However, the origin of "nanoconfinement effects" on the glassy dynamics of thin films, where gradients from different interfaces interact and genuine collective finite size effects may emerge, remains a longstanding open question. Here, we combine molecular dynamics simulations, probing 5 decades of relaxation, and the Elastically Cooperative Nonlinear Langevin Equation (ECNLE) theory, addressing 14 decades in timescale, to establish a microscopic and mechanistic understanding of the key features of altered dynamics in freestanding films spanning the full range from ultrathin to thick films. Simulations and theory are in qualitative and near-quantitative agreement without use of any adjustable parameters. For films of intermediate thickness, the dynamical behavior is well predicted to leading order using a simple linear superposition of thick-film exponential barrier gradients, including a remarkable suppression and flattening of various dynamical gradients in thin films. However, in sufficiently thin films the superposition approximation breaks down due to the emergence of genuine finite size confinement effects. ECNLE theory extended to treat thin films captures the phenomenology found in simulation, without invocation of any critical-like phenomena, on the basis of interface-nucleated gradients of local caging constraints, combined with interfacial and finite size-induced alterations of the collective elastic component of the structural relaxation process.

Functional-renormalization-group approach to classical liquids with short-range repulsion: A scheme without repulsive reference system.

The renormalization-group approaches for classical liquids in previous works required a repulsive reference such as a hard-core one when applied to systems with short-range repulsion. The need for the reference is circumvented here by using a functional-renormalization-group approach for integrating the hierarchical flow of correlation functions along a path of variable interatomic coupling. We introduce the cavity distribution functions to avoid the appearance of divergent terms and choose a path to reduce the error caused by the decomposition of higher order correlation functions. We demonstrate using exactly solvable one-dimensional models that the resulting scheme yields accurate thermodynamic properties and interatomic distribution at various densities when compared to integral-equation methods such as the hypernetted chain and the Percus-Yevick equation, even in the case where our hierarchical equations are truncated with the Kirkwood superposition approximation, which is valid for low-density cases.

Calculation of pair and triplet correlation functions for a Lennard-Jones fluid at ρ*≤1.41 and T*≤25

On the basis of Monte Carlo simulations, configurations and pair and triplet correlation functions for a Lennard-Jones fluid are reported over a large range of densities and temperatures (0.002 ≤ ρ* ≤ 1.41 and 0.45 ≤ T* ≤ 25, dimensionless). In total, data for 27 615 ρ*–T*-state points including 750 configurations for each state point are used for the calculation of the pair and triplet correlation functions. For the pair configuration function, an approximation over the whole set of state points is provided, which reproduces the pair configuration with high accuracy (3σ < 0.0075). The results for the triplet configuration functions are compared to the Kirkwood superposition approximation. With the exception of low ρ* (<0.3), the application of the Kirkwood superposition approximation seems not to be a proper choice, showing errors >20%. The configurations and pair and triplet correlation functions of all simulations are openly accessible and can be used as a reference for future theoretical developments of Lennard-Jones fluids and, especially, the liquid state.

Implicit Solvation Using the Superposition Approximation (IS-SPA): Extension to Peptides in a Polar Solvent.

Efficient, accurate, and adaptable implicit solvent models remain a significant challenge in the field of molecular simulation. A recent implicit solvent model, IS-SPA, based on approximating the mean solvent force using the superposition approximation, provides a platform to achieve these goals. IS-SPA was originally developed to handle nonpolar solutes in a polar solvent and did not accurately capture polar solvation. Here, we demonstrate that IS-SPA can accurately capture polar solvation by incorporating solvent orientation and accounting for the contributions from long ranged electrostatics. Solvent orientation is approximated as that of an ideal dipole aligned in a mean electrostatic field and an analytic form of the long ranged electrostatics is derived. Parameters for the model are calculated from explicit solvent simulations of an isolated atom or molecule and include atom-based solvent densities, mean electric field functions, radially symmetric averaged Lennard-Jones forces, and multipoles of the explicit solvent model. Using these parameters, IS-SPA accounts for asymmetry of charge solvation and reproduces the explicit solvent potential of mean force of dimerization of two oppositely charged Lennard-Jones spheres in chloroform with high fidelity. Additionally, the model more accurately captures the effect of explicit solvent on the monomer and dimer configurations of alanine dipeptide in chloroform than a generalized Born or constant density dielectric model. The current version of the algorithm is expected to outperform explicit solvent simulations for aggregation of small peptides at concentrations below 150 mM, well above the typical experimental concentrations for these materials.