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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Replica symmetry breaking in spin glasses in the replica-free Keldysh formalism

We show that the algebra of Parisi ultrametric matrices is recovered by the real-time, replica-free, Dyson-Keldysh equations of infinite-range quantum spin glasses in the late time glassy limit. This connects to earlier results on classical and quantum systems showing how ultrametricity emerges from the persistent slow aging dynamics of the glass phase. The stationary spin glass state thereby spontaneously breaks thermal symmetry, or the Kubo-Martin-Schwinger relation of a state in global thermal equilibrium. We describe the Keldysh path integral of the infinite-range Ising model in transverse and longitudinal fields, and in the context of the Landau expansion of the action functional, show how the long-time limit connects to the full replica symmetry breaking obtained in the equilibrium formalism. We also illustrate our formalism by applying it to the spherical quantum p p -spin model, which only exhibits one-step replica symmetry breaking.

Lang, Johannes (ORCID:0000000283533392)↗
DOE OSTI2015

A generalized parallel replica dynamics

Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying stochastic process to a quasi-stationary distribution. Two requirements for applying parallel replica dynamics are knowledge of the time scale on which the process converges to the quasi-stationary distribution and a mechanism for generating samples from this distribution. By combining a Fleming–Viot particle system with convergence diagnostics to simultaneously identify when the process converges while also generating samples, we can address both points. This variation on the algorithm is illustrated with various numerical examples, including those with entropic barriers and the 2D Lennard-Jones cluster of seven atoms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Accelerating ring-polymer molecular dynamics with parallel-replica dynamics

Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe–Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

On the replica structure of Sachdev-Ye-Kitaev model

We investigate existence of replica off-diagonal solutions in the field-theoretical description of Sachdev-Ye-Kitaev model. To this end we evaluate a set of local and non-local dynamic correlation functions in the long time limit. We argue that the structure of the soft-mode Schwarzian action is qualitatively different in replica-diagonal vs. replica-off-diagonal scenarios, leading to distinct long-time predictions for the correlation functions. We then evaluate the corresponding correlation functions numerically and compare the simulations with analytical predictions of replica-diagonal and replica-off-diagonal calculations. We conclude that all our numerical results are in a quantitative agreement with the theory based on the replica-diagonal saddle point plus Schwarzian and massive Gaussian fluctuations (the latter do contain replica off-diagonal components). This seems to exclude any contributions from replica-off-diagonal saddle points, at least on the time scales shorter than the inverse many-body level spacing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Cost and Time Effective Lithography of Reusable Millimeter Size Bone Tissue Replicas With Sub‐15 nm Feature Size on A Biocompatible Polymer

Abstract The ability to replicate the microenvironment of biological tissues creates unique biomedical possibilities for stem cell applications. Current fabrication methods are limited by either the control on feature size and shape, or by the throughput and size of the replicas. Here, a novel platform is reported that combines thermal scanning probe lithography (tSPL) with innovative methodologies for the low‐cost and high‐throughput nanofabrication of large area quasi‐3D bone tissue replicas with high fidelity, sub‐15 nm lateral precision, and sub‐2 nm vertical resolution. This bio‐tSPL platform features a biocompatible polymer resist that withstands multiple cell culture cycles, allowing the reuse of the replicas, further decreasing costs and fabrication times. The as‐fabricated replicas support the culture and proliferation of human induced mesenchymal stem cells, which display broad therapeutic and biomedical potential. Furthermore, it is demonstrated that bio‐tSPL can be used to nanopattern the bone tissue replicas with amine groups, for subsequent tissue‐mimetic biofunctionalization. The achieved level of time and cost‐effectiveness, as well as the cell compatibility of the replicas, make bio‐tSPL a promising platform for the production of tissue‐mimetic replicas to study stem cell‐tissue microenvironment interactions, test drugs, and ultimately harness the regenerative capacity of stem cells and tissues for biomedical applications.

Liu, Xiangyu↗
DOE OSTI2025

Multi-invariants and bulk replica symmetry

In this paper, we analyze the question of replica symmetry in the bulk for multi-partite entanglement measures in the vacuum state of two dimensional holographic CFTs. We first define a class of multi-partite local unitary invariants, multi-invariants , with a given replica symmetry that acts freely and transitively on the replicas. We look for a subclass of measures such that the dual bulk geometry also preserves replica symmetry. We obtain the most general solution to this problem if we require the bulk to preserve replica symmetry for general configurations of the regions. Orbifolding the bulk solution with the replica symmetry gives us a bulk geometry with a network of conical singularities. Our approach makes it clear that there are infinitely many infinitely large families of multi-invariants such that each family evaluates identically on the holographic state. Geometrically, these are equalities involving volumes of handlebodies, possibly of different genus, at particular points in the moduli space. In certain cases, we check our bulk computation with an explicit calculation in CFT. Finally we comment on the generalization to higher dimension.

AdS-CFT Correspondence↗
DOE OSTI2018

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

We report that replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD algorithm for ligand binding, in which replicas along the alchemical thermodynamic coupling axis λ were expanded as a series of Hamiltonian boosted replicas along a second axis to form a two-dimensional (2D) replica-exchange exchange map [Jiang, W.; Roux, B., J. Chem. Theory Comput. 2010, 6 (9), 2559-2565]. Aiming to achieve a similar performance at a lower computational cost, we propose here a modified version of this algorithm in which only the end-states along the alchemical axis are augmented by boosted replicas. The reduced FEP/(λ,H)-REMD method with one-dimensional (1D) unbiased alchemical thermodynamic coupling axis λ is implemented on the basis of generic multiple copy algorithm (MCA) module of the biomolecular simulation program NAMD. The flexible MCA framework of NAMD enables a user to design customized replica-exchange patterns through Tcl scripting in the context of a highly parallelized simulation program without touching the source code. Two Hamiltonian tempering boosting scheme were examined with the new algorithm: a first one based on potential energy rescaling of a pre-identified “solute”, and a second one via the introduction of flattening torsional free energy barriers. As two illustrative examples with reliable experiment data, the absolute binding free energies of pxylene and n-butylbenzene to the nonpolar cavity of the L99A mutant of T4 lysozyme were calculated. Lastly, the tests demonstrate that the new protocol efficiently enhances the sampling of torsional motions for backbone and side chains around the binding pocket and accelerates the convergence of the free energy computations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4, 5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Interfacial Electron-Phonon Coupling Constants Extracted from Intrinsic Replica Bands in Monolayer FeSe/SrTiO 3

The observation of replica bands by angle-resolved photoemission spectroscopy has ignited interest in the study of electron-phonon coupling at low carrier densities, particularly in monolayer FeSe/SrTiO 3 , where the appearance of replica bands has motivated theoretical work suggesting that the interfacial coupling of electrons in the FeSe layer to optical phonons in the SrTiO 3 substrate might contribute to the enhanced superconducting pairing temperature. Alternatively, it has also been recently proposed that such replica bands might instead originate from extrinsic final state losses associated with the photoemission process. Here, we perform a quantitative examination of replica bands in monolayer FeSe/SrTiO 3 , where we are able to conclusively demonstrate that the replica bands are indeed signatures of intrinsic electron-boson coupling, and not associated with final state effects. A detailed analysis of the energy splittings and relative peak intensities between the higher-order replicas, as well as other self-energy effects, allows us to determine that the interfacial electron-phonon coupling in the system corresponds to a value of λ=0.19±0.02, providing valuable insights into the enhancement of superconductivity in monolayer FeSe/SrTiO 3 . The methodology employed here can also serve as a new and general approach for making more rigorous and quantitative comparisons to theoretical calculations of electron-phonon interactions and coupling constants.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Spurious long-range entanglement and replica correlation length

Topological entanglement entropy has been regarded as a smoking-gun signature of topological order in two dimensions, capturing the total quantum dimension of the topological particle content. An extrapolation method on cylinders has been used frequently to measure the topological entanglement entropy. Here in this paper, we show that a class of short-range entangled 2D states, when put on an infinite cylinder of circumference L , exhibits the entanglement Rényi entropy of any integer index α ≥ 2 that obeys S α = a L-γ , where α, γ > 0 . Under the extrapolation method, the subleading term γ would be identified as the topological entanglement entropy, which is spurious. A nonzero γ is always present if the 2D state reduces to a certain symmetry-protected topological 1D state, upon disentangling spins that are far from the entanglement cut. The internal symmetry that stabilizes γ > 0 is not necessarily a symmetry of the 2D state, but should be present after the disentangling reduction. If the symmetry is absent, γ decays exponentially in L with a characteristic length, termed as a replica correlation length, which can be arbitrarily large compared to the two-point correlation length of the 2D state. We propose a simple numerical procedure to measure the replica correlation length through replica correlation functions. We also calculate the replica correlation functions for representative wave functions of Abelian discrete gauge theories and the double semion theory in 2D, to show that they decay abruptly to zero. This supports a conjecture that the replica correlation length being small implies that the subleading term from the extrapolation method determines the total quantum dimension.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Storing files in a parallel computing system using list-based index to identify replica files

Improved techniques are provided for storing files in a parallel computing system using a list-based index to identify file replicas. A file and at least one replica of the file are stored in one or more storage nodes of the parallel computing system. An index for the file comprises at least one list comprising a pointer to a storage location of the file and a storage location of the at least one replica of the file. The file comprises one or more of a complete file and one or more sub-files. The index may also comprise a checksum value for one or more of the file and the replica(s) of the file. The checksum value can be evaluated to validate the file and/or the file replica(s). A query can be processed using the list.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Accelerating the Convergence of Replica Exchange Simulations Using Gibbs Sampling and Adaptive Temperature Sets

We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of relevant states through the whole ensemble of replicas. This mechanism depends on the knowledge of global thermodynamic functions which are measured during the simulation and not coupled to the heat bath temperatures driving the individual simulations. Therefore, this setup also allows for a continuous adaptation of the temperature set. In this paper, we will review the new scheme and demonstrate its capability. The method is particularly useful for the fast and reliable estimation of the microcanonical temperature T (U) or, equivalently, of the density of states g(U) over a wide range of energies.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica–Exchange

A systematic and statistically robust protocol is applied for the evaluation of free energy calculations with and without replica-exchange. The protocol is based on ensemble averaging to generate accurate assessments of the uncertainties in the predictions. Comparison is made between FEP+ and TIES—free energy perturbation and thermodynamic integration with enhanced sampling—the latter with and without the so-called “enhanced sampling” based on replica-exchange protocols. Standard TIES performs best for a reference set of targets and compounds; no benefits accrue from replica-exchange methods. Evaluation of FEP+ and TIES with REST—replica-exchange with solute tempering—reveals a systematic and significant underestimation of free energy differences in FEP+, which becomes increasingly large for long duration simulations, is confirmed by extensive analysis of previous publications, and raises a number of questions pertaining to the accuracy of the predictions with the REST technique not hitherto discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Multi-variance replica exchange SGMCMC for inverse and forward problems via Bayesian PINN

Physics-informed neural network (PINN) has been successfully applied in solving a variety of nonlinear non-convex forward and inverse problems. However, the training is challenging because of the non-convex loss functions and the multiple optima in the Bayesian inverse problem. In this work, we propose a multi-variance replica exchange stochastic gradient Langevin dynamics method to tackle the challenge of the multiple local optima in the optimization and the challenge of the multiple modal posterior distribution in the inverse problem. Replica exchange methods are capable of escaping from the local traps and accelerating the convergence; two chains with different temperatures are designed where the low temperature chain aims for the local convergence, and the target of the high temperature chain is to travel globally and explore the whole loss function entropy landscape. However, it may not be efficient to solve mathematical inversion problems by using the vanilla replica method directly since the method doubles the computational cost in evaluating the forward solvers (likelihood functions) in the two chains. To address this issue, we propose to make different assumptions on the energy function estimation and this facilities one to use solvers of different fidelities in the likelihood function evaluation. More precisely, one can use a solver with low fidelity in the high temperature chain while using a solver with high fidelity in the low temperature chain. Our proposed method significantly lowers the computational cost in the high temperature chain, meanwhile preserving the accuracy and converging very fast. Here we give an unbiased estimate of the swapping rate and give an estimation of the discretization error of the scheme. To verify our idea, we design and solve four inverse problems which have multiple modes. The proposed method is also employed to train the Bayesian PINN to solve the forward and inverse problems; faster and more accurate convergence has been observed when compared to the stochastic gradient Langevin dynamics (SGLD) method and vanilla replica exchange methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing

Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional molecular simulations to adequately visit the cis and trans structures. A replica-exchange method is presented that allows for easy rotations of the amide bond and also an efficient linking to a high temperature replica. The method allows for just three replicas (one at the temperature and Hamiltonian of interest, a second high temperature replica with a biased dihedral potential, and a third connecting them) to overcome the amide bond sampling problem and also enhance sampling for other coordinates. Here our results indicate that for short peptoid oligomers, the conformations can range from all cis to all trans with an average cis/trans ratio that depends on side chain and potential model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations

An implementation of the replica exchange with dynamical scaling (REDS) method in the commonly used molecular dynamics program GROMACS is presented. REDS is a replica exchange method that requires fewer replicas than conventional replica exchange while still providing data over a range of temperatures and can be used in either constant volume or constant pressure ensembles. Details for running REDS simulations are given, and an application to the human islet amyloid polypeptide (hIAPP) 11-25 fragment shows that the model efficiently samples conformational space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

High-order replica bands in monolayer FeSe/SrTiO3 revealed by polarization-dependent photoemission spectroscopy

Abstract The mechanism of the enhanced superconductivity in monolayer FeSe/SrTiO 3 has been enthusiastically studied and debated over the past decade. One specific observation has been taken to be of central importance: the replica bands in the photoemission spectrum. Although suggestive of electron-phonon interaction in the material, the essence of these spectroscopic features remains highly controversial. In this work, we conduct angle-resolved photoemission spectroscopy measurements on monolayer FeSe/SrTiO 3 using linearly polarized photons. This configuration enables unambiguous characterization of the valence electronic structure with a suppression of the spectral background. We consistently observe high-order replica bands derived from various Fe 3 d bands, similar to those observed on bare SrTiO 3 . The intensity of the replica bands is unexpectedly high and different between d xy and d yz bands. Our results provide new insights on the electronic structure of this high-temperature superconductor and the physical origin of the photoemission replica bands.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗