Accurate Potential Function Research Articles

Spectroscopic and Theoretical Identifications of Two Structural Motifs of (H2O)10 Cluster.

Precise characterization of archetypal systems of aqueous hydrogen-bonding networks is essential for developing accurate potential functions and universal models of water. The structures of water clusters (H2O)n (n = 2-9) have been verified recently through size-specific infrared spectroscopy with a vacuum ultraviolet free electron laser (VUV-FEL) and quantum chemical studies. For (H2O)10, the pentagonal prism and butterfly motifs were proposed to be important building blocks and were observed in previous experiments. Here we report the size-specific infrared spectra of (H2O)10 via a joint experimental and theoretical study. Well-resolved spectra provide a unique signature for the coexistence of pentagonal prism and butterfly motifs. These (H2O)10 motifs develop from the dominant structures of (H2O)n (n = 8, 9) clusters. This work provides an intriguing prelude to the diverse structure of liquid water and opens avenues for size-dependent measurement of larger systems to understand the stepwise formation mechanism of hydrogen-bonding networks.

Molecular Dynamics Simulation Studies of Properties, Preparation, and Performance of Silicon Carbide Materials: A Review

Silicon carbide (SiC) materials are widely applied in the field of nuclear materials and semiconductor materials due to their excellent radiation resistance, thermal conductivity, oxidation resistance, and mechanical strength. The molecular dynamics (MD) simulation is an important method to study the properties, preparation, and performance of SiC materials. It has significant advantages at the atomic scale. The common potential functions for MD simulations of silicon carbide materials were summarized firstly based on extensive literatures. The key parameters, complexity, and application scope were compared and analyzed. Then, the MD simulation of SiC properties, preparation, and performance was comprehensively overviewed. The current studies of MD simulation methods and applications of SiC materials were systematically summarized. It was found that the Tersoff potential was the most widely applied potential function for the MD simulation of SiC materials. The construction of more accurate potential functions for special application fields was an important development trend of potential functions. In the MD simulation of SiC properties, the thermal properties and mechanical properties, including thermal conductivity, hardness, elastic modulus, etc., were mainly studied. The correlation between MD simulations of microscopic processes and the properties of macroscopic materials, as well as the methods for obtaining different property parameters, were summarized. In the MD simulation of SiC preparation, ion implantation, polishing, sputtering, deposition, crystal growth, amorphization, etc., were mainly studied. The chemical vapor deposition (CVD) and sintering methods commonly applied in the preparation of SiC nuclear materials were reported rarely and needed to be further studied. In the MD simulation of SiC performance, most of the present studies were related to SiC applications in the nuclear energy research. The irradiation damage simulation in the field of nuclear materials was studied most widely. It can be found that SiC materials in the field of nuclear materials study were a very important topic. Finally, the future perspective of MD simulation studies of SiC materials were given, and development suggestions were summarized. This paper is helpful for understanding and mastering the general method of computation material science aimed at the multi-level analysis. It also has a good reference value in the field of SiC material study and MD method study.

The absorption spectrum of short-lived isotopic variant of water, H215O: Tentative detection at the Earth's atmosphere

A calculated infrared vibration–rotation spectrum of isotopically modified water, H215O, is presented. Oxygen-15 has a half-life of about 2 minutes and H215O may be formed in the atmosphere during thunderstorms as a result of photonuclear processes or when the atmosphere is irradiated by cosmic γ-rays. Variational nuclear motion calculations of vibrational and vibrational-rotational levels up to 25000 cm−1 and up to J = 10 in angular momentum are performed within the framework of the Born-Oppenheimer approximation using an accurate water potential function. The line shape parameters for H215O are estimated. Spectral ranges that are promising for the detection of H215O in the atmosphere are identified and a search for spectral signatures conducted. A spectral feature is tentatively assigned to the 752 (0 1 0) - 643 (0 0 0) line of H215O.

Eighth-order virial equation of state and speed-of-sound measurements for krypton.

An eighth-order virial equation of state (VEOS) for krypton, valid for temperatures up to 5000 K, was developed using the accurate potential functions proposed by Jäger et al. [J. Chem. Phys. 144, 114304 (2016)] for the pair interactions and nonadditive three-body interactions between krypton atoms. While the second and third virial coefficients were already calculated by Jäger et al., the fourth- to eighth-order coefficients were determined in the present work. A simple analytical function was fitted individually to the calculated values of each virial coefficient to obtain the VEOS in an easy-to-use analytical form. To enable a stringent test of the quality of the new VEOS, we measured the speed of sound in krypton in the temperature range from 200 K to 420 K and at pressures up to 100 MPa with a very low uncertainty (at the 0.95 confidence level) of 0.005%-0.018% employing the pulse-echo technique. In order to verify that the isotopic composition of the krypton sample conforms to that of natural krypton in air, high-precision measurements of krypton isotope ratios using a high-sensitivity noble gas mass spectrometer were performed. The extensive comparison with the new speed-of-sound data as well as with experimental p-ρ-T and speed-of-sound data from the literature indicates that pressures and speeds of sound calculated using our new VEOS have uncertainties (at the 0.95 confidence level) of less than 0.1% at state points at which the VEOS is sufficiently converged.

Hydrophobic Effect: The Entropic Structure of the Protein Hydration Interface

Characterizing the interactions between protein and water is quintessential to protein folding and dynamics. As the driving force of protein folding, the hydrophobic effect is mainly characterized by burial of non-polar surface area that indirectly measures the increase in water entropy. A more direct approach is to understand how polar and nonpolar residues arrange on the protein surface in a way to maximize the entropy of solvating water, which minimizes the chemical potential of overall folded protein system. At the protein-water interface, distribution of hydrophilic and hydrophobic groups determines the arrangement of water molecules, which directly relates to the water entropy. In maximizing water entropy, proteins need to minimally disturb water's hydrogen bonding network by presenting interfaces very close to water: the polar group distribution on the protein surface should mimic the bulk water structure. To investigate water entropy, many near native protein structures in water were simulated using molecular dynamics. A dynameomics library of over 400 protein domains were run using the CHARMM force field implemented in the NAMD package. The distribution of pairwise polar atom distances connected through the hydrogen bonding network of waters were collected and analyzed. The polar group distribution holds a striking resemblance to the radial distribution function of bulk water. The distribution of polar groups are also classified depending upon the secondary structure, and are also categorized according to the nature of the polar group atoms such as side chain atoms and backbone atoms. Because these results imply that the entropy of water can be directly calculated from the distribution of polar groups on the protein surface, this research provides a stepping-stone in developing more accurate potential functions to describe solvation free energies of proteins.

Vitrification and Density Scaling of Polyurea at Pressures up to 6 GPa

Elastomeric polyurea is an important polymer for impact mitigation, but viscoelasticity, nonlinearity, pressure-effects, and the onset of the glass transition complicate analyses of experimental measurements. Consequently, development efforts rely on modeling, which in turn requires accurate potential functions. To address this issue, we measured the glass transition, Tg, of polyurea at pressures up to 6 GPa in a diamond anvil cell. In this method, Tg is determined as the lowest temperature at which the pressure is hydrostatic. From the pressure dependence of Tg, in combination with equation of state measurements at pressures up to 1 GPa, the density scaling exponent for the polyurea was obtained. The value 2.39 ± 0.06 is in accord with previous determinations based on lower pressure experiments; thus, density scaling remains valid for density changes as large as 50%. The scaling exponent reflects the steepness of the intermolecular repulsive potential and should serve as a guide to the choice of potentia...

Evaluation of the GROMOS 56ACARBO Force Field for the Calculation of Structural, Volumetric, and Dynamic Properties of Aqueous Glucose Systems.

Glucose is an important carbohydrate, relevant both for its biological functions and as a raw material for industrial processes. As a monomer of cellulose, the most abundant biopolymer, it is an alternative feedstock for fuels and chemicals in the biorefinery framework. Since glucose is often used and processed in aqueous solutions, it is important to understand the structural, volumetric, and dynamic properties of aqueous glucose solutions at varying concentrations. Molecular dynamics (MD) simulations are an effective means for computing the properties of liquid solutions, but the technique relies upon accurate intermolecular potential functions (i.e., "force fields"). Here we evaluate the accuracy of the recently developed GROMOS 56ACARBO glucose force field for its ability to model the density, viscosity, and self-diffusivity of aqueous glucose solutions as a function of concentration. We also compute different structural properties, including hydrogen bonds, radial and spatial distribution functions, and coordination numbers. The results show that the force field accurately models the density and viscosity of dilute solutions up to a glucose mole fraction of 0.1. At higher glucose concentrations, the force field overestimates the experimental density and viscosity. By analyzing the liquid structure, it is found that the glucose molecules tend to associate at higher concentrations, which leads to deviation from the experimental results. This suggests that, while the GROMOS 56ACARBO force field performs well for highly dilute glucose solutions (conditions under which it was developed), it is not appropriate for carrying out simulations of more concentrated glucose solutions. It is possible to obtain much more accurate densities and viscosities at high glucose concentrations by uniformly reducing the partial charges on glucose by 20%, which attenuates the self-association tendencies of glucose.

The foundation and study of a new type of lattice inversion potential for Iridium

In this paper, the lattice cohesive curve of iridium is investigated through first-principles calculations. The double-exponential function to fit the curve is presented. The inversion pair potential curve is generated through Chen’s inversion method. The accurate pair potential function is obtained through fitting by the new double-exponential function. The phonon spectra are calculated using the inversion potential data, the embedded atom method (EAM) potential theory and first-principles method, respectively, to verify the reliability of the inversion potential. The method combining Boltzmann statistics equation with accuracy fitting of lattice cohesive energy curve is proposed to calculate the thermal expansion coefficient. In addition, the bulk modulus and Grüneisen constant in the room temperature are calculated. The results are in good agreement with experiment results, which imply that the inversion potential is effective and accurate.

Application and foundation on inversion lattice potential of gold and silver

How to construct an accurate interatomic potential function is an important and basic problem in the simulation procedure. Using first-principles method, the single atom energies in different lattice constants are calculated to achieve the ground state curves of Au and Ag. These energies are calculated in the Perdew and Zunger form of the local-density approximation ultra-soft pseudo potentials. The cut-off energies of the plane wave bases of Au and Ag are set to be 320 eV and 300 eV respectively, which are sufficient for their full converge. The Brillouin zone is all sampled with a 12×12×12 Monkhorst-Pack mesh of k points for Au and Ag. Allowable error in total energy is smaller than 1×10-6 eV per atom. The lattice cohesive energies in different lattice constants are calculated to achieve the lattice energy and atom distance curves after subtracting the value of ground state energy from each of these energy. Then the accurate inversion potential curves are obtained according to the Chen-Möbius inversion theory and self-compiled program. Based on the fitting consequences of inversion potential curves, using different potential function formulas, a double exponential potential function to fit the inversion potential is presented. This function provides the accurate formulas and parameters for the following research. Moreover, the phonon spectra and the densities of states of Au and Ag are calculated respectively by using the inversion potential data, the embedded atom method (EAM) potential theory and first principles method to verify the reliability of the inversion potential. The comparison of the results among the three methods shows that the tendencies of these curves are similar. But they still have some deviations especially in the range of high frequency. However these curves indicate that the inversion potential can reasonably reflect the interaction between atoms. Meanwhile, the inversion potential method has great advantage in calculation quantity compared with the EAM potential method. The inversion method needs less time in calculation. In addition, the thermal expansion coefficients, the elastic moduli and the Grüneisen constants of Au and Ag are also calculated based on the fitting formulas and parameters. The results agree well with the experimental data, which implies that these inversion potentials are effective and accurate.

Pauli–Rydberg–London Potential: An Accurate Pair Potential Function for Diatomic Systems

Based on a molecular-orbital theory for H2(+), we have proposed and tested a pair potential function form for the diatomic systems. The new form has included the Pauli repulsive term, Rydberg potential, and London inverse-sixth-power energy, and is accurate at all relevant distances and simple enough for practical application in all-atom computer simulations. We find that an "approximate" universal reduced potential curve for strongly and weakly bound diatomic molecules may exist.

Development of a Polarizable Force Field for Macromolecules Based on the Classical Drude Oscillator

Accurate potential functions based on simple and computationally tractable functional forms are essential for meaningful molecular dynamics simulation studies of biomolecular systems. Towards this need we have developed a polarizable force field based on the classical Drude oscillator model. Built on a foundation of parameters optimized targeting a range of experimental and quantum mechanical (QM) data for small molecules representative of macromolecules, force fields for proteins, lipids, nucleic acids and carbohydrates have been developed. Extension of the polarizable model from small molecules to macromolecules required additional optimization of the electrostatic parameters in the context of the biopolymers, iterative optimization of the torsion potentials targeting both QM and experimental data and the inclusion of pair specific Lennard-Jones parameters. Examples from optimization of the polarizable model for proteins and nucleic acids will be presented, including results from explicit solvent simulations of 100 ns and longer.

Ion Channel Simulation with Explicit Solvent and Lipid Membrane Based on the Drude Polarizable Force Field

Accurate potential functions based on simple and computationally tractable functional forms are critical for meaningful MD simulation studies of ion channels based on atomic models. These systems are particularly challenging due to the large magnitude of the interactions involved and the contrasting features of the various molecular components. Water molecules provide a high dielectric bulk environment while the nonpolar hydrocarbon core of the lipid bilayer provides a low dielectric environment that surrounds the protein channel. The energetics of ion transport results from a delicate balance of very large ion-water and ion-protein interactions. These large energies are often in sharp contrast with the small activation energies, on the order of a few kBT, deduced from experimentally observed ion-fluxes. In the present work, a polarizable force field based on the classical Drude oscillator model was developed to enable all-atom MD simulations of biological ion channels. A systematic hierarchical strategy was used to optimize the parameters for water, ions, proteins, and lipids to best represent a collection of gas and liquid properties on the basis of small molecules representative of relevant functional groups. Ion models were optimized to reproduce both microscopic quantum mechanical and thermodynamic solvation data. Using MD simulations, a protein force field was tested for suite of peptides and proteins, and models of DPPC, DPPE, POPC and DOPC were tested against the experimental properties of bilayer membranes. First results from MD simulations of the KcsA channel embedded in a phospholipid bilayer with explicit solvent will be described.

An accurate pair potential function for diatomic systems

Based on the molecular-orbital theory for a simplest single-electron diatomic system, we have developed a unique functional form for pair potentials. We have demonstrated that the diatomic potential thus constructed is able to adequately describe a stable as well as meta-stable diatomic system with a good accuracy for all relevant internuclear distances.

On the X1Σ+rovibrational spectrum of lithium hydride

The complete line list of rovibrational transitions of the X 1 Σ + state of LiH is computed. The line list includes all possible dipoleallowed transition energies and oscillator strengths that cover the transition energy range 3.27−19476 cm −1 . The line list was obtained using an accurate potential and dipole moment function constructed from available experimental and theoretical data. This paper discusses the agreement of the current calculations with previous theoretical and experimental results. We also provide the radiative cooling function in the high-density limit over a wide temperature range and compare them with previous results. A simulated collisionally-broadened LiH opacity relevant to cool dwarf stars is also presented.

A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction.

BackgroundAn accurate potential function is essential to attack protein folding and structure prediction problems. The key to developing efficient knowledge-based potential functions is to design reference states that can appropriately counteract generic interactions. The reference states of many knowledge-based distance-dependent atomic potential functions were derived from non-interacting particles such as ideal gas, however, which ignored the inherent sequence connectivity and entropic elasticity of proteins.MethodologyWe developed a new pair-wise distance-dependent, atomic statistical potential function (RW), using an ideal random-walk chain as reference state, which was optimized on CASP models and then benchmarked on nine structural decoy sets. Second, we incorporated a new side-chain orientation-dependent energy term into RW (RWplus) and found that the side-chain packing orientation specificity can further improve the decoy recognition ability of the statistical potential.SignificanceRW and RWplus demonstrate a significantly better ability than the best performing pair-wise distance-dependent atomic potential functions in both native and near-native model selections. It has higher energy-RMSD and energy-TM-score correlations compared with other potentials of the same type in real-life structure assembly decoys. When benchmarked with a comprehensive list of publicly available potentials, RW and RWplus shows comparable performance to the state-of-the-art scoring functions, including those combining terms from multiple resources. These data demonstrate the usefulness of random-walk chain as reference states which correctly account for sequence connectivity and entropic elasticity of proteins. It shows potential usefulness in structure recognition and protein folding simulations. The RW and RWplus potentials, as well as the newly generated I-TASSER decoys, are freely available in http://zhanglab.ccmb.med.umich.edu/RW.

Thermodynamic properties of sea air

Abstract. Very accurate thermodynamic potential functions are available for fluid water, ice, seawater and humid air covering wide ranges of temperature and pressure conditions. They permit the consistent computation of all equilibrium properties as, for example, required for coupled atmosphere-ocean models or the analysis of observational or experimental data. With the exception of humid air, these potential functions are already formulated as international standards released by the International Association for the Properties of Water and Steam (IAPWS), and have been adopted in 2009 for oceanography by IOC/UNESCO. In this paper, we derive a collection of formulas for important quantities expressed in terms of the thermodynamic potentials, valid for typical phase transitions and composite systems of humid air and water/ice/seawater. Particular attention is given to equilibria between seawater and humid air, referred to as "sea air" here. In a related initiative, these formulas will soon be implemented in a source-code library for easy practical use. The library is primarily aimed at oceanographic applications but will be relevant to air-sea interaction and meteorology as well. The formulas provided are valid for any consistent set of suitable thermodynamic potential functions. Here we adopt potential functions from previous publications in which they are constructed from theoretical laws and empirical data; they are briefly summarized in the appendix. The formulas make use of the full accuracy of these thermodynamic potentials, without additional approximations or empirical coefficients. They are expressed in the temperature scale ITS-90 and the 2008 Reference-Composition Salinity Scale.

Knowledge-based potentials in protein fold recognition

An accurate potential function is essential for protein folding problem and structure prediction. Two different types of potential energy functions are currently in use. The first type is based on the law of physics and second type is referred to as statistical potentials or knowledge based potentials. In the latter type, the energy function is extracted from statistical analysis of experimental data of known protein structures. By increasing the amount of three dimensional protein structures, this approach is growing rapidly. There are various forms of knowledge based potentials depending on how statistics are calculated and how proteins are modeled. In this review, we explain how the knowledge based potentials are extracted by using known protein structures and briefly compare many of the potentials in theory.

Study of vibro-acoustography with high spatial resolution based on sector array transducers

This study investigates the vibro-acoustography of sector array transducers. Based on the vibro-acoustography and basic sector-array field theory, a modified and accurate velocity potential function is obtained. We further calculated and simulated the point spread function （PSF） of the system, designed the phantom of tissue, and simulated the phantom imaging. In the end, the influencing factors on spatial resolution with sector array transducers are analyzed on the basis of the simulation results. The results reveal that high resolution and contrast can be achieved, and this imaging method is of great value in detecting thermal lesion after high intensity ultrasound surgery and so on. The resolution will be improved by increasing central frequency, reducing geometric focal distance, and using transducers with larger aperture size.

Investigation of Silicon Model Nanotubes as Potential Candidate Nanomaterials for Efficient Hydrogen Storage: A Combined Ab Initio/Grand Canonical Monte Carlo Simulation Study

Grand canonical Monte Carlo (GCMC) simulations combined with ab initio QM calculations were employed to study the adsorption capacity of H2 in single-walled silicon nanotubes (SWSiNTs) of a hypothetical armchair structural model. The interaction energy of H2 with a graphite-like sheet from the surface of a single SiNT obtained from the QM calculations was fitted to an accurate potential function used to simulate the system. This theoretical approach is also used in SWCNTs of similar characteristics and at the same thermodynamic states. The GCMC simulation of NT bundles with H2 showed enhancement of H2 adsorptivity of SiNTs, as compared with CNTs. Concretely, the (14, 14) SWSiNTs present remarkable percentage improvement of 100, 70, 44, and 25% in the gravimetric (weight percent) adsorption of H2 at 293 K and 0.1, 1.0, 5.0, and 10.0 MPa, respectively, as compared with isodiameter (22, 22) CNTs. This is attributed to the stronger attractive interaction of H2 with SiNTs as compared to CNTs, found from the fi...

Beyond the Lennard-Jones model: a simple and accurate potential function probed by high resolution scattering data useful for molecular dynamics simulations

Scattering data, measured for rare gas-rare gas systems under high angular and energy resolution conditions, have been used to probe the reliability of a recently proposed interaction potential function, which involves only one additional parameter with respect to the venerable Lennard-Jones (LJ) model and is hence called Improved Lennard-Jones (ILJ). The ILJ potential eliminates most of the inadequacies at short- and long-range of the LJ model. Further reliability tests have been performed by comparing calculated vibrational spacings with experimental values and calculated interaction energies at short-range with those obtained from the inversion of gaseous transport properties. The analysis, extended also to systems involving ions, suggests that the ILJ potential model can be used to estimate the behavior of unknown systems and can help to assess the different role of the leading interaction components. Moreover, due to its simple formulation, the physically reliable ILJ model appears to be particularly useful for molecular dynamics simulations of both neutral and ionic systems.