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DOE OSTI2023

Shadow Molecular Dynamics and Atomic Cluster Expansions for Flexible Charge Models

Here, a shadow molecular dynamics scheme for flexible charge models is presented where the shadow Born–Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, is modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born–Oppenheimer molecular dynamics (BOMD). XL-BOMD provides stable dynamics while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO 2 ) and a molecular system of liquid water. The combined ACE+XL-QEq molecular dynamics simulations are stable over a wide range of temperatures both for the oxide and for the molecular systems and provide a precise sampling of the Born–Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO 2 , predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Temperature-dependent anisotropic magnetoresistance and spin-torque-driven vortex dynamics in a single microdisk

Spin-orbit-torque-driven dynamics have recently gained interest in the field of magnetism due to the reduced requirement of current densities and an increase in efficiency, as well as the ease of implementation of different devices and materials. From a practical point of view, the low-frequency dynamics below 1GHz is particularly interesting since dynamics associated with magnetic domains lie in this frequency range. While spin-torque excitation of high-frequency modes has been extensively studied, the intermediate low-frequency dynamics have received less attention, although spin torques could potentially be used for both manipulation of the spin texture and the excitation of dynamics. In this paper, we demonstrate that it is possible to drive magnetic vortex dynamics in a single microdisk by spin-Hall torque at varying temperatures and relate the results to transport properties. We find that the gyrotropic mode of the core couples to the low-frequency microwave signal and produces a measurable voltage. The dynamic measurements are in agreement with magnetic transport measurements and are supported by micromagnetic simulations. Our results open the door for integrating magnetic vortex devices in spintronic applications.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Tree tensor network hierarchical equations of motion based on time-dependent variational principle for efficient open quantum dynamics in structured thermal environments

In this work, we introduce an efficient method, TTN-HEOM, for exactly calculating the open quantum dynamics for driven quantum systems interacting with highly structured bosonic baths by combining the tree tensor network (TTN) decomposition scheme with the bexcitonic generalization of the numerically exact hierarchical equations of motion (HEOM). The method yields a series of quantum master equations for all core tensors in the TTN that efficiently and accurately capture the open quantum dynamics for non-Markovian environments to all orders in the system–bath interaction. These master equations are constructed based on the time-dependent Dirac–Frenkel variational principle, which isolates the optimal dynamics for the core tensors given the TTN ansatz. The dynamics converges to the HEOM when increasing the rank of the core tensors, a limit in which the TTN ansatz becomes exact. We introduce TENSO, tensor equations for non-Markovian structured open systems, as a general-purpose Python code to propagate the TTN-HEOM dynamics. We implement three general propagators for the coupled master equations: two fixed-rank methods that require a constant memory footprint during the dynamics and one adaptive-rank method with a variable memory footprint controlled by the target level of computational error. We exemplify the utility of these methods by simulating a two-level system coupled to a structured bath containing one Drude–Lorentz component and eight Brownian oscillators, which is beyond what can presently be computed using the standard HEOM. Our results show that the TTN-HEOM is capable of simulating both dephasing and relaxation dynamics of driven quantum systems interacting with structured baths, even those of chemical complexity, with an affordable computational cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Shadow molecular dynamics for flexible multipole models

Shadow molecular dynamics provide an efficient and stable atomistic simulation framework for flexible charge models with long-range electrostatic interactions. Shadow molecular dynamics simulations are driven by approximate “shadow” Born–Oppenheimer potentials for which the exact charges and forces are directly accessible without relying on costly (and approximate) iterative solvers. While previous implementations have been limited to atomic monopole charge distributions, we extend this approach to flexible multipole models. We derive detailed expressions for the shadow energy functions, potentials, and force terms, explicitly incorporating monopole–monopole, dipole–monopole, and dipole–dipole interactions. In our formulation, both atomic monopoles and atomic dipoles are treated as extended dynamical variables alongside the propagation of the nuclear degrees of freedom. We demonstrate that introducing the additional dipole degrees of freedom preserves the stability and accuracy previously seen in monopole-only shadow molecular dynamics simulations. In addition, we present a shadow molecular dynamics scheme where the monopole charges are held fixed while the dipoles remain flexible. Our extended shadow dynamics provide a framework for stable, computationally efficient, and versatile molecular dynamics simulations involving long-range interactions between flexible multipoles. This is of particular current interest in combination with machine-learned interatomic potentials, including long-range electrostatic interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Ab initio ultrafast spin dynamics in solids

Spin relaxation and decoherence is at the heart of spintronics and spin-based quantum information science. Currently, theoretical approaches that can accurately predict spin relaxation of general solids including necessary scattering pathways and are capable of nanosecond to millisecond simulation time are urgently needed. We present a first-principles real-time density-matrix approach based on Lindblad dynamics to simulate ultrafast spin dynamics for general solid-state systems. Through the complete first-principles descriptions of pump, probe, and scattering processes including electron-phonon, electron-impurity, and electron-electron scatterings with self-consistent electronic spin-orbit couplings, our method can directly simulate the ultrafast pump-probe measurements for coupled spin and electron dynamics over nanoseconds at any temperatures and doping levels. We first apply this method to a prototypical system GaAs and obtain excellent agreement with experiments. We found that the relative contributions of different scattering mechanisms and phonon modes differ considerably between spin and carrier relaxation processes. In sharp contrast to previous work based on model Hamiltonians, we point out that the electron-electron scattering is negligible at room temperature but becomes dominant at low temperatures for spin relaxation in n-type GaAs. We further examine ultrafast dynamics in novel spin-valleytronic materials: monolayer and bilayer WSe 2 with realistic defects. We find that spin relaxation is highly sensitive to local symmetry and chemical bonds around defects. For the bilayer WSe 2 , we identify the scattering pathways in ultrafast dynamics and determine relevant dynamical properties, essential to its utilization of unique spin-valley-layer locking effects. In conclusion, our work provides a predictive computational platform for spin dynamics in solids, which has potential for designing new materials ideal for spintronics and quantum information technology.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

A dynamic variational multiscale method on unstructured meshes for stationary transport problems

Here, this paper presents a variational multiscale (VMS) based finite element method where the stabilization parameter is computed dynamically. The current dynamic procedure takes in a general structure/form of the stabilization parameter with unknown coefficients and computes them dynamically in a local fashion resulting in a dynamic VMS-based finite element method. Thus, a static stabilization parameter with pre-defined coefficients is not needed. A variational Germano identity (VGI) based local procedure suitable for unstructured meshes is developed to perform the dynamic computation in a local fashion. The local VGI based procedure is applied for each interior vertex in the mesh and unknown coefficients are first determined locally at each vertex, and subsequently, for each element a maximum value is taken over the vertices of the element. To make the current procedure practical, a coarser secondary solution is constructed from the primary coarse-scale solution, which is done locally over a patch of elements around each interior vertex. Further, averaging steps are employed to make the local dynamic procedure robust. Currently, the new dynamic VMS formulation is applied to steady problems governed by the advection-diffusion and incompressible Navier-Stokes equations in both 1D and 2D to demonstrate its efficacy and effectiveness.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Viscoelastic necking dynamics between attractive microgels

Hypothesis: Microgels can deform and interpenetrate and display colloid/polymer duality. The effective interaction of microgels in the collapsed state is governed by the interplay of polymer–solvent interfacial tension and bulk elasticity. A connecting neck is shown to mediate microgel interaction, but its temporal evolution has not been addressed. Here we hypothesize that the necking dynamics of attractive microgels exhibits liquid-like or solid-like behavior over different time and length scales. Experiments: We simulate the merging and pinching of attractive microgels with different crosslinking densities in explicit solvent using dissipative particle dynamics. The temporal coalescence dynamics of microgels is investigated and compared with simple liquid and polymeric droplets. We model the neck growth on long time scales using Maxwell model of polymer relaxation and compare the theoretical prediction with simulation data. The mechanical strength of the neck is characterized systematically via simulated pinch-off of microgels by steered molecular dynamics. Findings: We evidence a crossover in the coalescence dynamics reflecting the viscoelastic signature of microgels. In contrast to the common knowledge that viscoelastic materials respond elastically on short time scales, the early expansion of the microgel neck exhibits a linear behavior, similar to the viscous coalescence of liquid droplets. However, the late regime with arrested dynamics resembles sintering of solid particles. Through an analytical model relating microgel dynamics to neck growth, we show that the long-term behavior is governed by stress relaxation of the polymers in the neck region and predict an exponential decay in the rate of growth, which agrees favorably with the simulation. Different from coalescence, the thread thinning in microgel breakup primarily highlights its polymeric characteristics.

42 ENGINEERING↗

DOE OSTI2025

Probing the Self-Assembly dynamics of cellulose nanocrystals by X-ray photon correlation spectroscopy

Charge-stabilized colloidal cellulose nanocrystals (CNCs) can self-assemble into higher-ordered chiral nematic structures by varying the volume fraction. The assembly process exhibits distinct dynamics during the isotropic to liquid crystal phase transition, which can be elucidated using X-ray photon correlation spectroscopy (XPCS). Anionic CNCs were dispersed in propylene glycol (PG) and water spanning a range of volume fractions, encompassing several phase transitions. Coupled with traditional characterization techniques, XPCS was conducted to monitor the dynamic evolution of the different phases. Additionally, simulated XPCS results were obtained using colloidal rods and compared with the experimental data, offering additional insights into the dynamic behavior of the system. The results indicate that the particle dynamics of CNCs undergo a stepped decay in three stages during the self-assembly process in PG, coinciding with the observed phases. The phase transitions are associated with a total drop of Brownian diffusion rates by four orders of magnitude, a decrease of more than a thousand times slower than expected in an ideal system of repulsive Brownian rods. Given the similarity in the phase behaviors in CNCs dispersed in PG and in water, we hypothesize that these dynamic behaviors can be extrapolated to other polar solvent environments. Importantly, these findings represent the direct measurement of CNC dynamics using XPCS, underscoring the feasibility of directly assessing the dynamic behavior of other rod-like colloidal suspensions.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Anomalous fast atomic dynamics in bulk metallic glasses

It is believed that the strong glass formers tend to be dense packing and have rather slow atomic dynamics. Here, we report that the anomalous fast atomic dynamics exist in an Au 55 Cu 20 Ag 5 Si 20 metallic glass (MG) with good glass forming ability (GFA) by combining X-ray photon correlation spectroscopy measurements with ab initio molecular dynamics simulations. The fast dynamics are mainly originated from the increased mobility of Cu atoms by Ag addition. Ag atoms are inclined to locate at Cu-centered <0, 2, 8, 1> motifs, which slow or accelerate the dynamics of shell Cu atoms, depending on whether Ag atoms appear at the first shells or not, leading to the formation of structural heterogeneity at the atomic level. The results enrich the understanding of atomic dynamics in Cue-Ag-containing MGs and will trigger more studies on the dynamics-GFA relationship in MGs.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Unpacking the drivers of diurnal dynamics of sun-induced chlorophyll fluorescence (SIF): Canopy structure, plant physiology, instrument configuration and retrieval methods

Sun-induced chlorophyll fluorescence (SIF) from spaceborne sensors is a promising tool for global carbon cycle monitoring, but its application is constrained by insufficient understanding of the drivers underlying diurnal SIF dynamics. SIF measurements from ground-based towers can reveal diurnal SIF dynamics across biomes and environmental conditions; however, meaningful interpretation of diurnal variations requires disentangling impacts from canopy structure, plant physiology, instrument configuration and retrieval methods, which often interact with and confound each other. This study aims to unpack these drivers using 1) concurrent ground and airborne canopy-scale and leaf-scale measurements at a corn field, 2) a mechanistic SIF model that explicitly considers the dynamics of photochemistry (via the fraction of open photosystem II reaction centers, qL) and photoprotection (via nonphotochemical quenching, NPQ) as well as their interactive dependence on the sub-canopy light environment, and 3) cross-comparison of SIF instrument configurations and retrieval methods. We found that crop row orientations and sun angles can introduce a distinctive midday dip in SIF in absence of stress, due to a midday drop of absorbed photosynthetically active radiation (APAR) when crop rows are north-south oriented. Canopy structure caused distinctive responses in both qL and NPQ at different positions within the vertical canopy that collectively influenced fluorescence quantum yield (Φ F ) at the leaf scale. Once integrated at the canopy scale, diurnal dynamics of both APAR and canopy escape probability (ε) are critical for accurately shaping diurnal SIF variations. While leaf-level qL and NPQ exhibited strong diurnal dynamics, their influence was attenuated at the canopy scale due to opposing effects on SIF at different canopy layers. Furthermore, different system configurations (i.e., bi-hemispherical vs. hemispherical-conical) and retrieval methods can bias the SIF magnitude and distort its diurnal shapes, therefore confounding the interpretation of inherent strength and dynamics of SIF emission. Our findings demonstrate the importance of crop row structures, interactive variations in canopy structure and plant physiology, instrument configuration, and retrieval method in shaping the measured dynamics of diurnal SIF. This study highlights the necessity to account for these factors to accurately interpret satellite SIF, and informs future synthesis work with different SIF instrumentation and retrieval methods across sites.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Dynamics of Water in Gemini Surfactant-Based Lyotropic Liquid Crystals

The dynamics of water confined to nanometer-sized domains is important in a variety of applications ranging from proton exchange membranes to crowding effects in biophysics. In this work we study the dynamics of water in gemini surfactant-based lyotropic liquid crystals (LLCs) using molecular dynamics simulations. These systems have well characterized morphologies, e.g., hexagonal, gyroid, and lamellar, and the surfaces of the confining regions can be controlled by modifying the headgroup of the surfactants. This allows one to study the effect of topology, functionalization, and interfacial curvature on the dynamics of confined water. Through analysis of the translational diffusion and rotational relaxation we conclude that the hydration level and resulting confinement lengthscale is the predominate determiner of the rates of water dynamics, and other effects, namely surface functionality and curvature, are largely secondary. In conclusion, this novel analysis of the water dynamics in these LLC systems provides an important comparison for previous studies of water dynamics in lipid bilayers and reverse micelles.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Backbone Dynamics of Bottlebrush Polymers Studied by Neutron Scattering

Bottlebrush polymers have a versatile architecture that is highly customizable due to the combination of a linear backbone and side chains. As a result of the chemical tethering of the side chains, both parts cannot be easily be separated. Huge effort is seen regarding the dynamical behavior of the side chains or the entire bottlebrush polymer, whereas few studies are available considering the backbone. Here, isotopic labeling in combination with quasi-elastic neutron scattering was used to compare the dynamical behavior of the bottlebrush’s backbone with the side chain dynamics. Keeping the side chains deuterated, (h-PNB)- g -(d-PPO), leads to the scattering signal dominated by backbone dynamics, while the fully protonated sample, (h-PNB)- g -(h-PPO), gives side chain dynamics. Both results reveal slower dynamics associated with the backbone with less heterogeneity, as seen for the side chains. Additionally, a plasticizer effect for the backbone dynamics is confirmed by extracting the glass transition temperature and comparing it with pure linear PNB.

neutron scattering↗

DOE OSTI2026

Local Chain Dynamics in Sequence-Controlled Polymers as a Tunable Handle for Rare Earth Sequestration

Chain dynamics govern the intricate behaviors of proteins, underpinning functions such as catalysis, recognition, and stimulus response, and are an increasingly appreciated aspect of structure–function relationships. Analogously, manipulating chain dynamics and structure in abiotic polymers via sequence control is an exciting, yet underexplored, strategy for improving material functions. In this work, we report a systematic study relating the sequence of polymeric sequestrants to their structure and dynamics, as well as to their binding affinity and selectivity for model substrates, rare earth elements (REEs). A series of sequence-controlled polymers with metal chelating, solubilizing, and structure forming monomers was synthesized via multiblock polymerization, yielding compositionally identical polymers with spectroscopically resolved domains and distinct morphologies. Using a combination of small-angle X-ray scattering and 19 F NMR relaxometry measurements, we connected differences in polymer structure and dynamics to polymer sequence variables such as the patchiness (density) of the structure forming monomer and the location of the chelating monomer. Furthermore, we found that, relative to calcium, all polymers in the series collapse more and have slower dynamics when binding REEs (lanthanum and lutetium) , though the extent of these effects were sequence-dependent and localized to specific domains within the polymer. Notably, sequence-controlled polymers that exhibited the largest conformational and dynamic changes upon binding REEs also bound REEs with the greatest affinity and modest selectivity. Collectively, these results correlate monomer patterning with dynamics, morphology, and REE binding performance en route to the development of efficient and selective macromolecular chelators.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Water Dynamics in Gyroid Phases of Self-Assembled Gemini Surfactants

Water-mediated ion transport through functional nanoporous materials depends on the dynamics of water confined within a given nanostructured morphology. In this study, we investigate hydrogen-bonding dynamics of interfacial water within a ‘normal’ (Type I) lyotropic gyroid phase formed by a gemini dicarboxylate surfactant self-assembly using a combina- tion of 2DIR spectroscopy and molecular dynamics simulations. Experiments and simulations demonstrate that water dynamics in the normal gyroid phase is one order of magnitude slower than that in bulk water, due to specific interactions between water, the ionic surfactant headgroups, and counterions. However, the dynamics of water in the normal gyroid phase are faster than those of water confined in a reverse spherical micelle of a sulfonate surfactant, given that the water pool in the reverse micelle and the water pore in the gyroid phase have roughly the same diameters. This difference in confined water dynamics likely arises from the significantly reduced curvature- induced frustration at the convex interfaces of the normal gyroid, as compared to the concave interfaces of a reverse spherical micelle. These detailed insights into confined water dynamics may guide the future design of artificial membranes that rapidly transport protons and other ions.

36 MATERIALS SCIENCE↗

DOE OSTI2014

First principles molecular dynamics without self-consistent field optimization

We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Dynamic heterogeneity in the folding/unfolding transitions of FiP35

Molecular dynamics simulations have become an important tool in studying protein dynamics over the last few decades. Atomistic simulations on the order of micro- to milliseconds are becoming feasible and are used to study the state-of-the-art experiments in atomistic detail. Yet, analyzing the high-dimensional-long-temporal trajectory data is still a challenging task and sometimes leads to contradictory results depending on the analyses. To reveal the dynamic aspect of the trajectory, here we propose a simple approach which uses a time correlation function matrix and apply to the folding/unfolding trajectory of FiP35 WW domain [Shaw et al., Science 330, 341 (2010)]. The approach successfully characterizes the slowest mode corresponding to the folding/unfolding transitions and determines the free energy barrier indicating that FiP35 is not an incipient downhill folder. The transition dynamics analysis further reveals that the folding/unfolding transition is highly heterogeneous, e.g., the transition path time varies by ∼100 fold. We identify two misfolded states and show that the dynamic heterogeneity in the folding/unfolding transitions originates from the trajectory being trapped in the misfolded and half-folded intermediate states rather than the diffusion driven by a thermal noise. The current results help reconcile the conflicting interpretations of the folding mechanism and highlight the complexity in the folding dynamics. This further motivates the need to understand the transition dynamics beyond a simple free energy picture using simulations and single-molecule experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

A new class of ensemble conserving algorithms for approximate quantum dynamics: Theoretical formulation and model problems

We develop two classes of quasi-classical dynamics that are shown to conserve the initial quantum ensemble when used in combination with the Feynman-Kleinert approximation of the density operator. These dynamics are used to improve the Feynman-Kleinert implementation of the classical Wigner approximation for the evaluation of quantum time correlation functions known as Feynman-Kleinert linearized path-integral. As shown, both classes of dynamics are able to recover the exact classical and high temperature limits of the quantum time correlation function, while a subset is able to recover the exact harmonic limit. A comparison of the approximate quantum time correlation functions obtained from both classes of dynamics is made with the exact results for the challenging model problems of the quartic and double-well potentials. It is found that these dynamics provide a great improvement over the classical Wigner approximation, in which purely classical dynamics are used. In a special case, our first method becomes identical to centroid molecular dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗