Four-site Model Research Articles

Building Water Models Compatible with Charge Scaling Molecular Dynamics.

Charge scaling has proven to be an efficient way to account in a mean-field manner for electronic polarization by aqueous ions in force field molecular dynamics simulations. However, commonly used water models with dielectric constants over 50 are not consistent with this approach leading to "overscaling", i.e., generally too weak ion-ion interactions. Here, we build water models fully compatible with charge scaling, i.e., having the correct low-frequency dielectric constant of about 45. To this end, we employ advanced optimization and machine learning schemes in order to explore the vast parameter space of four-site water models efficiently. As an a priori unwarranted positive result, we find a sizable range of force field parameters that satisfy the above dielectric constant constraint providing at the same time accuracy with respect to experimental data comparable with the best existing four-site water models such as TIP4P/2005, TIP4P-FB, or OPC. The present results thus open the way to the development of a consistent charge scaling force field for modeling ions in aqueous solutions.

Critical behavior in a chiral molecular model.

Understanding the condensed-phase behavior of chiral molecules is important in biology as well as in a range of technological applications, such as the manufacture of pharmaceuticals. Here, we use molecular dynamics simulations to study a chiral four-site molecular model that exhibits a second-order symmetry-breaking phase transition from a supercritical racemic liquid into subcritical D-rich and L-rich liquids. We determine the infinite-size critical temperature using the fourth-order Binder cumulant, and we show that the finite-size scaling behavior of the order parameter is compatible with the 3D Ising universality class. We also study the spontaneous D-rich to L-rich transition at a slightly subcritical temperature of T = 0.985Tc, and our findings indicate that the free energy barrier for this transformation increases with system size as N2/3, where N is the number of molecules, consistent with a surface-dominated phenomenon. The critical behavior observed herein suggests a mechanism for chirality selection in which a liquid of chiral molecules spontaneously forms a phase enriched in one of the two enantiomers as the temperature is lowered below the critical point. Furthermore, the increasing free energy barrier with system size indicates that fluctuations between the L-rich and D-rich phases are suppressed as the size of the system increases, trapping it in one of the two enantiomerically enriched phases. Such a process could provide the basis for an alternative explanation for the origin of biological homochirality. We also conjecture the possibility of observing nucleation at subcritical temperatures under the action of a suitable chiral external field.

Benchmarking of force fields to characterize the intrinsically disordered R2-FUS-LC region

Intrinsically Disordered Proteins (IDPs) play crucial roles in numerous diseases like Alzheimer's and ALS by forming irreversible amyloid fibrils. The effectiveness of force fields (FFs) developed for globular proteins and their modified versions for IDPs varies depending on the specific protein. This study assesses 13 FFs, including AMBER and CHARMM, by simulating the R2 region of the FUS-LC domain (R2-FUS-LC region), an IDP implicated in ALS. Due to the flexibility of the region, we show that utilizing multiple measures, which evaluate the local and global conformations, and combining them together into a final score are important for a comprehensive evaluation of force fields. The results suggest c36m2021s3p with mTIP3p water model is the most balanced FF, capable of generating various conformations compatible with known ones. In addition, the mTIP3P water model is computationally more efficient than those of top-ranked AMBER FFs with four-site water models. The evaluation also reveals that AMBER FFs tend to generate more compact conformations compared to CHARMM FFs but also more non-native contacts. The top-ranking AMBER and CHARMM FFs can reproduce intra-peptide contacts but underperform for inter-peptide contacts, indicating there is room for improvement.

Generation of thermal scattering laws with the CINEL code

The thermal scattering laws (TSL) take into account the crystalline structure and atomic motions of isotopes bound in materials. This paper presents the CINEL code, which was developed to generate temperature-dependent TSL for solid, liquid and free gas materials of interest for nuclear reactors. CINEL is able to calculate TSL from the phonon density of states (PDOS) of materials under the Gaussian-Incoherent approximations. The PDOS can be obtained by using theoretical approaches (e.g., ab initio density functional theory and molecular dynamics) or experimental results. In this work, the PDOS presented in the ENDF/BVIII.0 and NJOY-NCrystal libraries were used for numerical validation purposes. The CINEL results are in good agreement with those reported in these databases, even in the specific cases of TSL with the newly mixed elastic format. The coding flexibility offered by Python using the JupyterLab interface allowed to investigate limits of physical models reported in the literature, such as a four-site model for UO2, anharmonic behaviors of oxygen atoms bound in a Fm3m structure, texture in Zry4 samples and jump corrections in a roto-translational diffusion model for liquid water. The use of graphic processing units (GPU) is a necessity to perform calculations in a few minutes. The performances of the CINEL code is illustrated with the results obtained on actinide oxides having a Fm3m structure (UO2, ThO2, NpO2 and PuO2), low enriched fuel (UMo), cladding (Zry4) and moderators (H2O with a specific emphasis on ice).

Transmission across non-Hermitian -symmetric quantum dots and ladders

A non-Hermitian (NH) region connected to semi-infinite Hermitian lattices acts either as a source or as a sink and the probability current is not conserved in a scattering typically. Even a -symmetric region that contains both a source and a sink does not lead to current conservation plainly. We propose a model and study the scattering across a NH -symmetric two-level quantum dot (QD) connected to two semi-infinite one-dimensional lattices in a special way so that the probability current is conserved. Aharonov–Bohm type phases are included in the model, which arise from magnetic fluxes () through two loops in the system. We show that when , the probability current is conserved. We find that the transmission across the QD can be perfect in the -unbroken phase (corresponding to real eigenenergies of the isolated QD) whereas the transmission is never perfect in the -broken phase (corresponding to purely imaginary eigenenergies of the QD). The two transmission peaks have the same width only for special values of the fluxes (being odd multiples of ). In the broken phase, the transmission peak is surprisingly not at zero energy. We give an insight into this feature through a four-site toy model. We extend the model to a -symmetric ladder connected to two semi-infinite lattices. We show that the transmission is perfect in unbroken phase of the ladder due to Fabry–Pérot type interference, that can be controlled by tuning the chemical potential. In the broken phase of the ladder, the transmission is substantially suppressed.

The viscosity of liquid ethene: Measurement and molecular dynamic simulation

This work reports new experimental data and detailed equilibrium molecular dynamics (EMD) simulations of viscosity for liquid ethene. The measurements were carried out by using an improved vibrating-wire viscometer for temperatures from (173.150 to 233.150) K and pressures up to 5.5 MPa, with a combined expanded relative uncertainty of 5.3 % (k = 2). The experimental data were compared with the values calculated by the correlation of Holland et al. (with an uncertainty of 10 % for liquid), the deviations vary from − 7.2 % to 0.8 % and the AARD is 3.6 %. Furthermore, the Assael and Dymond scheme based on the hard-sphere model was used to correlate the experimental results with an AARD of 0.1 %. For understanding the structure and properties of liquid ethene at the molecular level, a comprehensive evaluation of ten different ethene force fields with four types of molecular configurations (two-site, three-site, four-site, and six-site models) was then performed to predict density and viscosity at a wide temperature range from (133.150 to 233.150) K and pressure of 5 MPa. The selected force fields were generally developed for the vapor–liquid equilibrium properties, without explicit consideration of viscosity and other transport properties. Overall, three rigid two-site force fields (SET, TraPPE-UA, and AUA4) gave the best predictions with the AARD within 0.32 % for density and 8.5 % for viscosity comparing with the correlations of Smukala et al. and Holland et al., separately. Mie force field with 16–6 potential and TraPPE-UA2 force field with two negative partial charges can accurately predict density but severely overestimate viscosity greater than 20 %. The larger intermolecular repulsion and electrostatic interaction may have contributed to the overestimation of viscosity especially at low temperatures.

Effective calculation of the Green's function in the time domain on near-term quantum processors

We propose an improved quantum algorithm to calculate the Green's function through real-time propagation, and use it to compute the retarded Green's function for the 2-, 3- and 4-site Hubbard models. This novel protocol significantly reduces the number of controlled operations when compared to those previously suggested in literature. Such reduction is quite remarkable when considering the 2-site Hubbard model, for which we show that it is possible to obtain the exact time propagation of the $|N\pm 1\rangle$ states by exponentiating one single Pauli component of the Hamiltonian, allowing us to perform the calculations on an actual superconducting quantum processor.

Fluid-fluid phase transitions in a chiral molecular model.

Molecular chirality is a fundamental phenomenon, underlying both life as we know it and industrial pharmaceutical syntheses. Understanding the symmetry breaking phase transitions exhibited by many chiral molecular substances provides basic insights for topics ranging from the origin of life to the rational design of drug manufacturing processes. In this work, we have performed molecular dynamics simulations to investigate the fluid-fluid phase transitions of a flexible three-dimensional four-site chiral molecular model developed by Latinwo et al. [J. Chem. Phys. 145, 154503 (2016)] and Petsev et al. [J. Chem. Phys. 155, 084105 (2021)]. By introducing a bias favoring local homochiral vs heterochiral interactions, the system exhibits a phase transition from a single achiral phase to a single chiral phase that undergoes infrequent interconversion between the two thermodynamically identical chiral states: the L-rich and D-rich phases. According to the phase rule, this reactive binary system has two independent degrees of freedom and exhibits a density-dependent critical locus. Below the liquid-liquid critical locus, there exists a first-order vapor-liquid coexistence region with a single independent degree of freedom. Our results provide basic thermodynamic and kinetic insights for understanding many-body chiral symmetry breaking phenomena.

Hybrid quantum-classical algorithm for computing imaginary-time correlation functions

Quantitative descriptions of strongly correlated materials pose a considerable challenge in condensed matter physics and chemistry. A promising approach to address this problem is quantum embedding methods. In particular, the dynamical mean-field theory (DMFT) maps the original system to an effective quantum impurity model comprising correlated orbitals embedded in an electron bath. The biggest bottleneck in DMFT calculations is numerically solving the quantum impurity model, i.e., computing the Green's function. Past studies have proposed theoretical methods to compute the Green's function of a quantum impurity model in polynomial time using a quantum computer. So far, however, efficient methods for computing the imaginary-time Green's functions have not been established despite the advantages of the imaginary-time formulation. We propose a quantum-classical hybrid algorithm for computing imaginary-time Green's functions on quantum devices with limited hardware resources by applying the variational quantum simulation. Using a quantum circuit simulator, we verified this algorithm by computing Green's functions for a dimer model as well as a four-site impurity model obtained by DMFT calculations of the single-band Hubbard model, although our method can be applied to general imaginary-time correlation functions.

Effects of fluid–solid interaction strength on wetting of graphite-like substrates by water: density functional theory

We have explored wetting of graphite-like substrates by water using density functional approach for classical associating fluids. The four-site fluid water model without electrostatic interactions has been taken from Clark et al. [Molec. Phys. 2006, 104, 3561]. The fluid–solid potential is assumed to have a 10-4-3 functional form. The interaction strength is considered as a free parameter. The growth of water film on the substrate upon changing chemical potential is described. The wetting and prewetting critical temperatures, as well as the prewetting phase diagram are evaluated for different fluid–solid attraction. Moreover, the temperature dependence of the contact angle is obtained from the Young equation. It yields estimations for the wetting temperature as well. Theoretical findings are compared with experimental results and with data from computer simulations. The theory is successful and quite accurate in describing the wetting temperature and contact angle changes with temperature and fluid–substrate attraction. Moreover, it provides tools to study other associating fluids on solids of importance for chemical engineering easier, in comparison to experiments and computer simulations.

The genetic polymorphisms of key genes in WNT pathway (LRP5 and AXIN1) was associated with osteoporosis susceptibility in Chinese Han population.

Genetic factors play a critical role in the pathogenesis of osteoporosis. The imbalance of WNT/β-catenin will cause the occurrence of osteoporosis. LRP5 and AXIN1 play an important role in the classical Wnt/β-catenin signaling pathway. Our study was aimed to determine the association between five candidate single nucleotide polymorphisms (SNPs) of LRP5 or AXIN1 and osteoporosis susceptibility in Chinese Han population. A total of 599 osteoporosis patients and 599 healthy individuals were recruited for this case-control study. Agena MassARRAY was used to genotype SNPs. The association between SNPs and osteoporosis susceptibility in different genetic models was analyzed by PLINK software. We used false-positive report probability (FPRP) analysis to detect whether the positive results were just chance or noteworthy observations. Multifactor dimension reduction (MDR) was used to analyze the interaction of SNP-SNP in the osteoporosis risk. Finally, haplotype analysis was performed by plink1.07 and Haploview software. We found that LRP5 rs11228240, AXIN1 rs2301522, and rs9921222 were significantly associated with the osteoporosis susceptibility. The results of subgroup analysis showed that LRP5 rs11228240 (protective factor) and AXIN1 rs2301522 (risk factor) were associated with the susceptibility of osteoporosis among participants who were age >60 years, female or BMI ≤ 24; AXIN1 rs9921222 significantly increased the risk of osteoporosis among participants with BMI ≤ 24. The genotype Ars2301522Crs9921222 could increase the susceptibility of osteoporosis (p = 0.026). The rs11228219LPR5, rs11228240 LPR5, rs2301522AXIN1, and rs9921222AXIN1 four-site model was the best model for predicting the osteoporosis risk (test accuracy = 0.541; CVC = 10/10). The LRP5-rs11228240, AXIN1-rs2301522, and AXIN1- rs9921222 were associated with osteoporosis susceptibility in Chinese Han population.

Molecular Dynamics Simulation of Phosphorus Trichloride (PCl3) and Phosphorus Triiodide (PI3) Liquids by Using the Force-fields Derived from a Quantum Chemical Approach

In this study, phosphorus trichloride (PCl3) and phosphorus triiodide (PI3) as the condensed inorganic materials were investigated based on the molecular dynamics simulation. To this purpose, molecular dynamics simulations were performed by applying force field parameters derived from the quantum chemistry approach. The potential energy data were computed at the B3LYP/6-31+G (d) and B3LYP/dgdzvpd levels of theory for different configurations of PCl3 and PI3, respectively. To determine force field parameters, a four-site all-atom force field model was used to correlate the potential energy data. Therefore, the force field parameters were applied to perform the molecular dynamics simulations. The MD simulations were performed to obtain the atomic number density, enthalpy, heat capacity, and radial distribution function in the NPT and NVT ensembles for PCl3 and PI3 dimers. There is a good consistency between the experimental data and simulation results over a wide range of experimental conditions.

Effect of configuration-dependent multi-body forces on interconversion kinetics of a chiral tetramer model

We describe a reformulation of the four-site molecular model for chiral phenomena introduced by Latinwo et al. ["Molecular model for chirality phenomena," J. Chem. Phys. 145, 154503 (2016)]. The reformulation includes an additional eight-body force that arises from an explicit configuration-dependent term in the potential energy function, resulting in a coarse-grained energy-conserving force field for molecular dynamics simulations of chirality phenomena. In this model, the coarse-grained interaction energy between two tetramers depends on their respective chiralities and is controlled by a parameter λ, where λ < 0 favors local configurations involving tetramers of opposite chirality and λ > 0 gives energetic preference to configurations involving tetramers of the same chirality. We compute the autocorrelation function for a quantitative chirality metric and demonstrate that the multi-body force modifies the interconversion kinetics such that λ ≠ 0 increases the effective barrier for enantiomer inversion. Our simulations reveal that for λ > 0 and temperatures below a sharply defined threshold value, this effect is dramatic, giving rise to spontaneous chiral symmetry breaking and locking molecules into their chiral identity.

Three- and four-site models for heavy water: SPC/E-HW, TIP3P-HW, and TIP4P/2005-HW.

Heavy water or deuterium oxide, D2O, is used as a solvent in various biophysical and chemical experiments. To model such experiments with molecular dynamics simulations, effective pair potentials for heavy water are required, which reproduce the well-known physicochemical differences relative to light water. We present three effective pair potentials for heavy water, denoted SPC/E-HW, TIP3P-HW, and TIP4P/2005-HW. The models were parameterized by modifying the widely used three- and four-site models for light water, with the aim of maintaining the specific characteristics of the light water models. At room temperature, SPC/E-HW and TIP3P-HW capture the modulations relative to light water of the mass and electron densities, heat of vaporization, diffusion coefficient, and water structure. TIP4P/2005-HW captures, in addition, the density of heavy water over a wide temperature range.

Atomic scale Monte-Carlo simulations of neutron diffraction experiments on stoichiometric uranium dioxide up to 1664 K

The neutron transport in nuclear fuels depends on the crystalline structure of materials when neutron energies lie below a few eV. For that purpose, the theoretical formalism that describes the neutron elastic and inelastic scatterings by crystals has been implemented in the CINEL processing tool in order to provide temperature-dependent neutron cross sections usable by the Monte-Carlo code TRIPOLI4®. The performances of the Monte-Carlo calculations are illustrated with the analysis of neutron powder diffraction data on UO2 measured up to 1664 K with the D4 and D20 diffractometers of the Institute Laue–Langevin (Grenoble, France). The comparison of the experimental and simulated pair distribution functions confirms the unusual decrease of the U–O atomic distances with increasing temperature when an ideal fluorite structure (Fm3̄m space group) with harmonic atomic vibrations is assumed over the full temperature range. The flexibility of the CINEL code allowed to explore disorder or anharmonic oxygen vibrations in the Fm3̄m space group by using either a four-site model with a relaxation term or a structure factor equation with a non-zero anharmonic third-cumulant coefficient. As none of these models succeeded to improve the agreement with the experiments, recent works that propose other local crystalline symmetries for UO2 at elevated temperatures were investigated with the CINEL code. The case of the Pa3̄ symmetry is briefly discussed in this paper.

Molecular dynamics simulations of lithium superionic conductor Li10GeP2S12 using a machine learning potential

The molecular dynamics simulations have been performed for tetragonal Li10GeP2S12 (LGPS) to investigate the Li-ion conductivity and underlying diffusion mechanism. The atomic interactions are simulated by the machine learning potential which provides accuracy comparable to ab-initio calculations and enable to collect statistics at root temperature. The obtained Li sites are consistent with the four-site model identified by the experiments. The Li-ion conductivity at 300 K and the activation energy are predicted to be σ = 12 mS/cm and Ea = 226 meV, respectively, which are in remarkable agreement with the experimental data. It is found that the ratio of the Li-ion diffusivity in the c direction to that in the ab plane is approximately three and the activation energies for both components are almost identical, suggesting a small anisotropy for Li-ion diffusion in LGPS. Our numerical experiment clearly indicates that the diffusion along the in-plane two-dimensional paths is the rate-limiting process in the overall diffusion.

Machine learning for reparameterization of four-site water models: TIP4P-BG and TIP4P-BGT.

Parameterizing an effective water model is a challenging issue because of the difficulty in maintaining a comprehensive balance among the diverse physical properties of water with a limited number of parameters. The advancement in machine learning provides a promising path to search for a reliable set of parameters. Based on the TIP4P water model, hence, about 6000 molecular dynamics (MD) simulations for pure water at 1 atm and in the range of 273-373 K are conducted here as the training data. The back-propagation (BP) neural network is then utilized to construct an efficient mapping between the model parameters and four crucial physical properties of water, including the density, vaporization enthalpy, self-diffusion coefficient and viscosity. Without additional time-consuming MD simulations, this mapping operation could result in sufficient and accurate data for high-population genetic algorithm (GA) to optimize the model parameters as much as possible. Based on the proposed parameterizing strategy, TIP4P-BG (a conventional four-site water model) and TIP4P-BGT (an advanced model with temperature-dependent parameters) are established. Both the water models exhibit excellent performance with a reasonable balance among the four crucial physical properties. The relevant mean absolute percentage errors are 3.53% and 3.08%, respectively. Further calculations on the temperature of maximum density, isothermal compressibility, thermal expansion coefficient, radial distribution function and surface tension are also performed and the resulting values are in good agreement with the experimental values. Through this water modeling example, the potential of the proposed data-driven machine learning procedure has been demonstrated for parameterizing a MD-based material model.

Understanding how water models affect the anomalous pressure dependence of their diffusion coefficients

The self-diffusion coefficient of water shows an anomalous increase with increasing hydrostatic pressure up to a broad maximum (PmD) near 1 kbar at 298 K, which has been attributed to pressure effects on the tetrahedral hydrogen bond network of water. Moreover, the ability of a water model to reproduce anomalous properties of water is a signature that it is reproducing the network. Here, water was simulated between 1 bar and 5 kbar using three water models, two four-site (with all charges in the molecular plane) and one single-site multipole (which accounts for out-of-molecular plane charge), that have reasonable pressure-temperature properties. For these three models, the diffusion coefficients display a maximum in the pressure dependence and the radial distribution functions show good agreement with the limited experimental structural data at high pressure that are available. In addition, a variety of properties associated with the network are examined, including hydrogen bond lifetimes and occupancies, three-body angle distributions, and tetrahedral order parameters. Results suggest that the initial increasing diffusion with pressure is because hydrogen bonds are distorted and thus weakened by pressure, but above PmD, the hydrogen bonds are weakened to the point it behaves more like a normal liquid. In other words, the PmD may be a measure of the angular strength of hydrogen bonds. In addition, since the four-site models over-predict the values of PmD while the multipole model under-predicts it, out-of-plane charge may improve four-site models.

A new correlation for viscosity of model water-carbon nanotube nanofluids: Molecular dynamics simulation

In the present study, the viscosity of a model water-based nanofluid including an armchair-type (6,6) single-wall carbon nanotube is examined via Molecular Dynamics Simulation. The flexible four-site water model and the Tersoff empirical interatomic potential model are employed as an intermolecular force between liquid water molecules and as an interatomic potential function of carbon nanotube, respectively. Nevertheless, the interactions among water‑carbon nanotube atoms are modeled by the Lennard-Jones potential. The viscosity of nanofluid is sought using the Green–Kubo method at temperatures of 273 K, 283 K, 293 K, 303 K, and 313 K with volume fractions of 0.418%, 0.557% and 0.6%. The results are assessed with the related experimental data. The Radial Distribution Function is also calculated for its importance and usage to link the microscopic and macroscopic data. In conclusion, a relationship is obtained for the viscosity of water‑carbon nanotube nanofluids,μ=BζmTAζn+ζCT, in which volume fraction, temperature and viscosity are linked to each other. The recommended correlation is revealed to be acceptable and accurate for volume fractions in the range of 0.25 % ≤ ϕ ≤ 0.65%.

Analysis of the behaviour of confined molecules using 2 H T 1 nuclear magnetic relaxation dispersion

ABSTRACT A four-site exchange model is developed in order to explain deuterium T 1 -nuclear magnetic relaxation dispersion (NMRD) profiles of acetonitrile in silica pore systems. The four-site exchange model comprises a bulk, surface and two types of burried or cavity sites. It is found that the residence time of acetonitrile- d 3 at a flat Si-surface is less than 100 ps. No bilayer-like ordering of acetonitrile is formed at the Si-surface because no quadrupole splitting was observed. The dispersion in the deuterium T1-NMRD profiles are due to relatively few so-called β-sites with molecular residence time in the range 0.2–2 micro seconds. This deuterium T 1 -NMR dispersion experiment suggest that the retention time of different analysts can be studied in terms of their residence time in β sites.