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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Electronic structure theory on modeling short-range noncovalent interactions between amino acids

While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the “gold standard” coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller−Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.

Chemistry↗
DOE OSTI2012

Universal relationships for the phonon spectra in BCC, FCC, and HCP crystals with a short-range interatomic interaction

The frequencies of the phonon branches that correspond to the vibrations of the close-packed atomic planes in bcc, fcc, and hcp crystals with short-range interatomic interaction are shown to be described by a universal relationship, which only contains two parameters for each branch, for any polarization {lambda}. These phonon branches correspond to the ({xi}, {xi}, 0) direction in bcc crystals, the ({xi}, {xi}, {xi}) direction in fcc crystals, and the (0, 0, {xi}) direction in hcp crystals. This universal relationship can only be violated by long-range interactions, namely, the interactions outside the sixth coordination shell in a bcc crystal, the fifth coordination shell in an fcc crystal, and the eleventh or tenth coordination shell in an hcp crystal. The effect of these long-range interactions for each phonon branch can be quantitatively characterized by certain parameters {Delta}{sub n{lambda}}, which are simply expressed in terms of the frequencies of three phonons of the branch. The values of these parameters are presented for all bcc, fcc, and hcp metals whose phonon spectra are measured. In most cases, the proposed relationships for the frequencies are found to be fulfilled accurate to several percent. In the cases where the {Delta}{sub n{lambda}} parameters are not small, they can give substantial information on the type and scale of long-range interaction effects in various metals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

A deep potential model with long-range electrostatic interactions

Machine learning models for the potential energy of multi-atomic systems, such as the deep potential (DP) model, make molecular simulations with the accuracy of quantum mechanical density functional theory possible at a cost only moderately higher than that of empirical force fields. However, the majority of these models lack explicit long-range interactions and fail to describe properties that derive from the Coulombic tail of the forces. To overcome this limitation, we extend the DP model by approximating the long-range electrostatic interaction between ions (nuclei + core electrons) and valence electrons with that of distributions of spherical Gaussian charges located at ionic and electronic sites. The latter are rigorously defined in terms of the centers of the maximally localized Wannier distributions, whose dependence on the local atomic environment is modeled accurately by a deep neural network. In the DP long-range (DPLR) model, the electrostatic energy of the Gaussian charge system is added to short-range interactions that are represented as in the standard DP model. The resulting potential energy surface is smooth and possesses analytical forces and virial. Missing effects in the standard DP scheme are recovered, improving on accuracy and predictive power. By including long-range electrostatics, DPLR correctly extrapolates to large systems the potential energy surface learned from quantum mechanical calculations on smaller systems. We illustrate the approach with three examples: the potential energy profile of the water dimer, the free energy of interaction of a water molecule with a liquid water slab, and the phonon dispersion curves of the NaCl crystal.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

A nine-dimensional ab initio global potential energy surface for the H{sub 2}O{sup +} + H{sub 2} → H{sub 3}O{sup +} + H reaction

An accurate full-dimensional global potential energy surface (PES) is developed for the title reaction. While the long-range interactions in the reactant asymptote are represented by an analytical expression, the interaction region of the PES is fit to more than 81 000 of ab initio points at the UCCSD(T)-F12b/AVTZ level using the permutation invariant polynomial neural network approach. Fully symmetric with respect to permutation of all four hydrogen atoms, the PES provides a faithful representation of the ab initio points, with a root mean square error of 1.8 meV or 15 cm{sup −1}. The reaction path for this exoergic reaction features an attractive and barrierless entrance channel, a submerged saddle point, a shallow H{sub 4}O{sup +} well, and a barrierless exit channel. The rate coefficients for the title reaction and kinetic isotope effect have been determined on this PES using quasi-classical trajectories, and they are in good agreement with available experimental data. It is further shown that the H{sub 2}O{sup +} rotational enhancement of reactivity observed experimentally can be traced to the submerged saddle point. Using our recently proposed Sudden Vector Projection model, we demonstrate that a rotational degree of freedom of the H{sub 2}O{sup +} reactant is strongly coupled with the reaction coordinate at this saddle point, thus unraveling the origin of the pronounced mode specificity in this reaction.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Long-Range Fit: A Software Package for the Representation and Study of Long-Range Molecular Interactions

Describing intermolecular forces is fundamental to modeling and predicting the behavior of molecular systems. In particular, long-range molecular interactions─with electrostatic, induction, and dispersion as the main components─play a critical role, especially for low-temperature and low-density regimes. Long-range interactions are often described through perturbation theory, representing the electronic charge distribution via a multipolar series of the moments and polarizability tensors corresponding to each molecule. However, while the theory is well established, obtaining the resulting analytical expressions (and their practical implementation) constitutes a highly complex and system-dependent task. To address this challenge, we developed long-range-fit (LRF), an interactive and user-friendly software package designed to automate the generation and fitting of long-range interaction terms for arbitrary molecules in nondegenerate (ground or excited) electronic states. We have derived and implemented all terms up to 15th order, without approximations, via a spherical tensor representation, with symmetry adaptation to all molecular point-group symmetries. The resulting potential energy surface is compatible with most representations of the close interaction region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random phase approximation

Despite their unmatched success for many applications, commonly used local, semi-local, and hybrid density functionals still face challenges when it comes to describing long-range interactions, static correlation, and electron delocalization. Density functionals of both the occupied and virtual orbitals are able to address these problems. The particle-hole (ph-) Random Phase Approximation (RPA), a functional of occupied and virtual orbitals, has recently known a revival within the density functional theory community. Following up on an idea introduced in our recent communication [H. van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501 (2013)], we formulate more general adiabatic connections for the correlation energy in terms of pairing matrix fluctuations described by the particle-particle (pp-) propagator. With numerical examples of the pp-RPA, the lowest-order approximation to the pp-propagator, we illustrate the potential of density functional approximations based on pairing matrix fluctuations. The pp-RPA is size-extensive, self-interaction free, fully anti-symmetric, describes the strong static correlation limit in H{sub 2}, and eliminates delocalization errors in H{sub 2}{sup +} and other single-bond systems. It gives surprisingly good non-bonded interaction energies – competitive with the ph-RPA – with the correct R{sup −6} asymptotic decay as a function of the separation R, which we argue is mainly attributable to its correct second-order energy term. While the pp-RPA tends to underestimate absolute correlation energies, it gives good relative energies: much better atomization energies than the ph-RPA, as it has no tendency to underbind, and reaction energies of similar quality. The adiabatic connection in terms of pairing matrix fluctuation paves the way for promising new density functional approximations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Laser-assisted free-free transition in electron-atom collisions

The free-free transition is studied for an electron-hydrogen atom system in the ground state at very low incident energies in the presence of an external homogeneous, monochromatic, and linearly polarized laser field. The incident electron is considered to be dressed by the laser field in a nonperturbative manner by choosing the Volkov solutions in both the initial and final channels. The space part of the scattering wave function for the electron is solved numerically by taking into account the effect of electron-exchange interactions, short-range interactions, as well as of long-range interactions. The laser-assisted differential as well as total elastic cross sections are calculated for single-photon absorption or emission in the soft photon limit, the laser intensity being much less than the atomic field intensity. A strong suppression is noted in the laser-assisted cross sections as compared to the field-free situations. A significant difference is noted in the singlet and the triplet cross sections.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

Electronic structures and magnetic stabilities of 2D Mn-doped GaAs nanosheets: The role of long-range exchange interactions and doping strategies

We investigate the structural, electronic and magnetic properties of Mn atoms doped two-dimensional (2D) hexagonal GaAs nanosheets (GaAsNSs) using both first-principle calculations and Monte Carlo simulations. The first-principle molecular dynamics is first used to test the structural stability of Mn-doped GaAsNS ((Ga,Mn)AsNS). The analysis of spin-resolved electronic structures and determination of magnetic exchange interactions based on density functional theory (DFT) calculations reveals the existence of long-range exchange interaction in the system. Finally, Metropolis Monte Carlo simulation is employed to estimate Curie temperatures (T{sub C}s) of (Ga,Mn)AsNSs with different doping concentrations by different doping strategies. The results indicate that a T{sub C} up to 82 K can be obtained in regularly-doped (Ga,Mn)AsNSs and doping strategies have prominent impact on T{sub C}s of the systems, which emphasizes the importance of both long-range interactions and doping strategies in reduced dimensional diluted magnetic semiconductors (DMSs)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

A superconducting quantum simulator based on a photonic-bandgap metamaterial

Synthesizing many-body quantum systems with various ranges of interactions facilitates the study of quantum chaotic dynamics. Such extended interaction range can be enabled by using nonlocal degrees of freedom such as photonic modes in an otherwise locally connected structure. Here, we present a superconducting quantum simulator in which qubits are connected through an extensible photonic-bandgap metamaterial, thus realizing a one-dimensional Bose-Hubbard model with tunable hopping range and on-site interaction. Using individual site control and readout, we characterize the statistics of measurement outcomes from many-body quench dynamics, which enables in situ Hamiltonian learning. Further, the outcome statistics reveal the effect of increased hopping range, showing the predicted crossover from integrability to ergodicity. Our work enables the study of emergent randomness from chaotic many-body evolution and, more broadly, expands the accessible Hamiltonians for quantum simulation using superconducting circuits.

Science & Technology - Other Topics↗
DOE OSTI2020

In-Situ Visualization of Long-Range Defect Interactions at the Edge of Melting

Connecting a bulk material’s microscopic defects to its macroscopic properties is an age-old problem in materials science. Long-range interactions between dislocations (line defects) are known to play a key role in how materials deform or melt, but we lack the tools to connect these dynamics to the macroscopic properties. We introduce time-resolved dark-field X-ray microscopy to directly visualize how dislocations move and interact over hundreds of micrometers, deep inside bulk aluminum. With real-time movies, we reveal the thermally activated motion and interactions of dislocations that comprise a boundary, and show how weakened binding forces inhomogeneously destabilize the structure at 99% of the melting temperature. Connecting dynamics of the microstructure to its stability, we provide important opportunities to guide and validate multiscale models that are yet untested.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Multilevel summation methods for efficient evaluation of long-range pairwise interactions in atomistic and coarse-grained molecular simulation.

The availability of efficient algorithms for long-range pairwise interactions is central to the success of numerous applications, ranging in scale from atomic-level modeling of materials to astrophysics. This report focuses on the implementation and analysis of the multilevel summation method for approximating long-range pairwise interactions. The computational cost of the multilevel summation method is proportional to the number of particles, N, which is an improvement over FFTbased methods who s cost is asymptotically proportional to N logN. In addition to approximating electrostatic forces, the multilevel summation method can be use to efficiently approximate convolutions with long-range kernels. As an application, we apply the multilevel summation method to a discretized integral equation formulation of the regularized generalized Poisson equation. Numerical results are presented using an implementation of the multilevel summation method in the LAMMPS software package. Preliminary results show that the computational cost of the method scales as expected, but there is still a need for further optimization.

Bond, Stephen D.↗
DOE OSTI2017

A generalized Ewald decomposition for screened Coulomb interactions

Medium-range interactions occur in a wide range of systems, including charged-particle systems with varying screening lengths. We generalize the Ewald method to charged systems described by interactions involving an arbitrary dielectric response function ϵ(𝐤). We provide an error estimate and optimize the generalization to find the break-even parameters that separate a neighbor list-only algorithm from the particle-particle particle-mesh algorithm. We examine the implications of different choices of the screening length for the computational cost of computing the dynamic structure factor. We then use our new method in molecular dynamics simulations to compute the dynamic structure factor for a model plasma system and examine the wave-dispersion properties of this system.

Dharuman, Gautham↗
DOE OSTI2013

Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

ChIP-based genome-wide assays of transcription factor (TF) occupancy have emerged as a powerful, high-throughput method to understand transcriptional regulation, especially on a global scale. This has led to great interest in the underlying biochemical mechanisms that direct TF-DNA binding, with the ultimate goal of computationally predicting a TF’s occupancy profile in any cellular condition. In this study, we examined the influence of various potential determinants of TF-DNA binding on a much larger scale than previously undertaken. We used a thermodynamics-based model of TF-DNA binding, called ‘‘STAP,’’ to analyze 45 TF-ChIP data sets from Drosophila embryonic development. We built a cross-validation framework that compares a baseline model, based on the ChIP’ed (‘‘primary’’) TF’s motif, to more complex models where binding by secondary TFs is hypothesized to influence the primary TF’s occupancy. Candidates interacting TFs were chosen based on RNA-SEQ expression data from the time point of the ChIP experiment. We found widespread evidence of both cooperative and antagonistic effects by secondary TFs, and explicitly quantified these effects. We were able to identify multiple classes of interactions, including (1) long-range interactions between primary and secondary motifs (separated by #150 bp), suggestive of indirect effects such as chromatin remodeling, (2) short-range interactions with specific inter-site spacing biases, suggestive of direct physical interactions, and (3) overlapping binding sites suggesting competitive binding. Furthermore, by factoring out the previously reported strong correlation between TF occupancy and DNA accessibility, we were able to categorize the effects into those that are likely to be mediated by the secondary TF’s effect on local accessibility and those that utilize accessibility-independent mechanisms. Finally, we conducted in vitro pull-down assays to test model-based predictions of short-range cooperative interactions, and found that seven of the eight TF pairs tested physically interact and that some of these interactions mediate cooperative binding to DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2010

Beyond Mean-Field Theories with Zero-Range Effective Interactions: A Way to Handle the Ultraviolet Divergence

Zero-range effective interactions are commonly used in nuclear physics and in other domains to describe many-body systems within the mean-field model. If they are used within a beyond-mean-field framework, contributions to the total energy that display an ultraviolet divergence are found. We propose a general strategy to regularize this divergence and we illustrate it in the case of the second-order corrections to the equation of state (EOS) of uniform symmetric matter. By setting a momentum cutoff {Lambda}, we show that for every (physically meaningful) value of {Lambda} it is possible to determine a new interaction such that the EOS with the second-order corrections reproduces the empirical EOS, with a fit of the same quality as that obtained at the mean-field level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Coherent exchange correlation in quantum systems

A number of exchange correlation effects in quantum systems are discussed from a unified point of view. These effects can be observed at both microscopic and macroscopic distances. The analysis of macroscopic correlation effects requires an understanding of the physical mechanism of exchange correlation. This, in turn, requires an analysis of the phase relationships between the wave functions of quantum states that determine the observed physical quantities. The neglect of these phase relationships in the interpretation of correlation experiments gave rise to assumptions such as instantaneous long-range interaction and other similar ideas that contradict the traditional physical principles of short-range interaction, causality, and locality. On the contrary, understanding the physical nature of the correlation mechanism makes it possible to explain these experiments without these kinds of ideas.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082–1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230–233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeler through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO-MD. - Highlights: • Electronic coarse graining unites many-body dispersion and polarisation beyond the dipole limit. • It consists of replacing the electrons of a molecule using a quantum harmonic oscillator, called a Quantum Drude Oscillator. • We present the first general implementation of Quantum Drude Oscillators in the molecular dynamics package QDO-MD. • We highlight the successful construction of a new, transferable molecular model of water: QDO-water. - Graphical abstract:.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

A fast mollified impulse method for biomolecular atomistic simulations

Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗