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At least 37 records · Page 2

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↗

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↗

Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space

We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of Wang-Landau and Replica-Exchange algorithms, and the one-dimensional version of this approach has been shown to be very efficient and to scale well, up to several thousands of computing cores. This approach allows us to split the parameter space of the system to be simulated into several pieces and still perform a random walk over the entire parameter range, ensuring the ergodicity of the simulation. Previous work, in which a similar scheme of parallel simulation was implemented without using replica exchange and with a different way to combine the result from the pieces, led to discontinuities in the final density of states over the entire range of parameters. From our simulations, it appears that the replica-exchange Wang-Landau algorithm is able to overcome this diculty, allowing exploration of higher parameter phase space by keeping track of the joint density of states.

Valentim, Alexandra↗

Implementation of replica-exchange umbrella sampling in GAMESS

In GAMESS-US quantum chemistry package, both replica-exchange molecular dynamics (REMD) and the umbrella sampling (US) methods are available. However, prior to this work, the replica-exchange umbrella sampling (REUS) method, combining REMD and US, was not implemented. Here, REUS affords a more efficient conformational sampling than the conventional US method and is often used in MD simulations. We implemented REUS in GAMESS-US and improved some routines of the existing REMD code. A density-functional tight-binding REMD (DFTB-REMD) simulation of alanine deca-peptide and a DFTB-MD REUS simulation of proton transfer in malonaldehyde were performed. The results of DFTB-MD REUS simulations performed with three different simulation packages were compared to validate our GAMESS-US implementation.

97 MATHEMATICS AND COMPUTING↗

Entanglement negativity and replica symmetry breaking in general holographic states

The entanglement negativity $\mathcal{E}$(A : B) is a useful measure of quantum entanglement in bipartite mixed states. In random tensor networks (RTNs), which are related to fixed-area states, it was found in ref. [1] that the dominant saddles computing the even Rényi negativity $\mathcal{E}$ (2k) generically break the ℤ 2k replica symmetry. This calls into question previous calculations of holographic negativity using 2D CFT techniques that assumed ℤ 2k replica symmetry and proposed that the negativity was related to the entanglement wedge cross section. In this paper, we resolve this issue by showing that in general holographic states, the saddles computing $\mathcal{E}$ (2k) indeed break the ℤ 2k replica symmetry.

AdS-CFT Correspondence↗

Replica wormholes and the black hole interior

Recent work has shown how to obtain the Page curve of an evaporating black hole from holographic computations of entanglement entropy. We show how these computations can be justified using the replica trick, from geometries with a spacetime wormhole connecting the different replicas. In a simple model, we study the Page transition in detail by summing replica geometries with different topologies. We compute related quantities in less detail in more complicated models, including JT gravity coupled to conformal matter and the SYK model. Separately, we give a direct gravitational argument for entanglement wedge reconstruction using an explicit formula known as the Petz map; again, a spacetime wormhole plays an important role. We discuss an interpretation of the wormhole geometries as part of some ensemble average implicit in the gravity description.

2D gravity↗

Analyticity of replica correlators and modular ETH

We study the two point correlation function of a local operator on an n -sheeted replica manifold corresponding to the half-space in the vacuum state of a conformal field theory. In analogy with the inverse Laplace transform, we define the Renyi transform of this correlation function, which is a function of one complex variable w, dual to the Renyi parameter n . Inspired by the inversion formula of Caron-Huot, we argue that if the Renyi transform ƒ(w) has bounded behavior at infinity in the complex w plane, the discontinuity of the Renyi transform disc ƒ(w) provides the unique analytic continuation in n of the original replica correlation function. We check our formula by explicitly calculating the Renyi transform of a particular replica correlator in a large N holographic CFT d in dimensions d > 2. We also discover that the discontinuity of the Renyi transform is related to the matrix element of local operators between two distinct eigenstates of the modular Hamiltonian. We calculate the Renyi transform in 2 d conformal field theories, and use it to extract the off-diagonal elements of (modular) ETH. We argue that in 2 d , this is equivalent to the off-diagonal OPE coefficients of a CFT and show that our technique exactly reproduces recent results in the literature.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Replica wormholes for an evaporating 2D black hole

Quantum extremal islands reproduce the unitary Page curve of an evaporating black hole. This has been derived by including replica wormholes in the gravitational path integral, but for the transient, evaporating black holes most relevant to Hawking’s paradox, these wormholes have not been analyzed in any detail. In this paper we study replica wormholes for black holes formed by gravitational collapse in Jackiw-Teitelboim gravity, and confirm that they lead to the island rule for the entropy. The main technical challenge is that replica wormholes rely on a Euclidean path integral, while the quantum extremal islands of an evaporating black hole exist only in Lorentzian signature. Furthermore, the Euclidean equations for the Schwarzian mode are non-local, so it is unclear how to connect to the local, Lorentzian dynamics of an evaporating black hole. We address these issues with Schwinger-Keldysh techniques and show how the non-local equations reduce to the local ‘boundary particle’ description in special cases.

2D gravity↗

Replica wormholes and the entropy of Hawking radiation

The information paradox can be realized in anti-de Sitter spacetime joined to a Minkowski region. In this setting, we show that the large discrepancy between the von Neumann entropy as calculated by Hawking and the requirements of unitarity is fixed by including new saddles in the gravitational path integral. These saddles arise in the replica method as complexified wormholes connecting different copies of the black hole. As the replica number n → 1, the presence of these wormholes leads to the island rule for the computation of the fine-grained gravitational entropy. We discuss these replica wormholes explicitly in two-dimensional Jackiw-Teitelboim gravity coupled to matter.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Real-time gravitational replicas: formalism and a variational principle

This work is the first step in a two-part investigation of real-time replica wormholes. Here we study the associated real-time gravitational path integral and construct the variational principle that will define its saddle-points. We also describe the general structure of the resulting real-time replica wormhole saddles, setting the stage for construction of explicit examples. These saddles necessarily involve complex metrics, and thus are accessed by deforming the original real contour of integration. However, the construction of these saddles need not rely on analytic continuation, and our formulation can be used even in the presence of non-analytic boundary-sources. Furthermore, at least for replica- and CPT-symmetric saddles we show that the metrics may be taken to be real in regions spacelike separated from a so-called ‘splitting surface’. This feature is an important hallmark of unitarity in a field theory dual.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Wormhole calculus, replicas, and entropies

We investigate contributions of spacetime wormholes, describing baby universe emission and absorption, to calculations of entropies and correlation functions, for example those based on the replica method. We find that the rules of the “wormhole calculus”, developed in the 1980s, together with standard quantum mechanical prescriptions for computing entropies and correlators, imply definite rules for limited patterns of connection between replica factors in simple calculations. These results stand in contrast with assumptions that all topologies connecting replicas should be summed over, and call into question the explanation for the latter. In a “free” approximation baby universes introduce probability distributions for coupling constants, and we review and extend arguments that successive experiments in a “parent” universe increasingly precisely fix such couplings, resulting in ultimately pure evolution. Once this has happened, the nontrivial question remains of how topology-changing effects can modify the standard description of black hole information loss.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Radiation induced amorphization of carbides in additively manufactured and conventional ferritic-martensitic steels: In-situ experiments on extraction replicas

In-situ irradiations using 1 MeV Kr 2+ ions in a transmission electron microscope were performed on extraction replica samples containing M 23 C 6 carbides and MX carbonitrides from two ferritic-martensitic (FM) steels: (i) 9%Cr-1%W-TaV based Eurofer97 and (ii) 9%Cr-1%Mo-VNb (all in wt.%) based additively manufactured (AM) Grade91 steel. The irradiations were performed between 100 and 773 K up to a maximum dose of ~2.4 displacements per atom (dpa). The M 23 C 6 carbides are highly susceptible to radiation induced amorphization (RIA), while the MX type nanoprecipitates are highly amorphization resistant across the entire irradiation temperature range. Between 100 and 423 K, RIA of M 23 C 6 carbides occurs very rapidly with critical amorphization doses ranging between ~0.35 and 0.9 dpa, increasing to higher doses at 573 K. Complete amorphization of the M 23 C 6 carbides up to doses of ~2.4 dpa is not possible at 773 K under the present irradiation conditions. The critical amorphization dose of M 23 C 6 carbides increases nearly exponentially with irradiation temperature. The critical temperature for the crystalline-to-amorphous phase transformation (T c→a ) of M 23 C 6 carbides irradiated as replica samples, i.e. without the surrounding metal matrix, was estimated to be ~812 K. Comparing the present results with neutron irradiation data on bulk samples reveals a decrease in the critical amorphization dose for M 23 C 6 and an increase of T c→a , highlighting the effect of dose rate on the amorphization behavior that is qualitatively consistent with literature on other non-metals. Changes in the minor chemistry of M 23 C 6 , such as presence or absence of W, V, Nb, Mo, seems to have little effect on the amorphization behavior. Here, in-situ irradiations on extraction replica samples provide a novel pathway to explore radiation tolerance of nanoprecipitates in nuclear structural materials

36 MATERIALS SCIENCE↗

Small-Angle X-ray Scattering Analysis of Colloidal Crystals and Replica Materials Made from L-Arginine-Stabilized Silica Nanoparticles

Colloidal crystals made from sub-100 nm silica nanoparticles have provided a versatile platform for the template-assisted synthesis of three-dimensionally interconnected semiconducting, metallic, and magnetic replicas. However, the detailed structure of these materials has not yet been characterized. Here, we investigated the structures of colloidal crystalline films and germanium replicas by scanning electron microscopy and small angle X-ray scattering. The structures of colloidal crystals made by evaporative assembly depends on the size of L-arginine-capped silica nanoparticles. Particles smaller than ~31 nm diameter assemble into non-close-packed arrangements (bcc) whereas particles larger than 31 nm assemble into random close-packed structures with disordered hexagonal phase. Polycrystalline films of these materials retain their structures and long-range order upon infiltration at high temperature and pressure, and the structure is preserved in Ge replicas. The shear force during deposition and dispersity of silica nanoparticles contributes to the size-based variation in the structure and to the size of crystal domains in the colloidal crystal films.

36 MATERIALS SCIENCE↗

Replica molding-based nanopatterning of tribocharge on elastomer with application to electrohydrodynamic nanolithography

Replica molding often induces tribocharge on elastomers. To date, this phenomenon has been studied only on untextured elastomer surfaces even though replica molding is an effective method for their nanotexturing. Here we show that on elastomer surfaces nanotextured through replica molding the induced tribocharge also becomes patterned at nanoscale in close correlation with the nanotexture. Here, by applying Kelvin probe microscopy, electrohydrodynamic lithography, and electrostatic analysis to our model nanostructure, poly(dimethylsiloxane) nanocup arrays replicated from a polycarbonate nanocone array, we reveal that the induced tribocharge is highly localized within the nanocup, especially around its rim. Through finite element analysis, we also find that the rim sustains the strongest friction during the demolding process. From these findings, we identify the demolding-induced friction as the main factor governing the tribocharge’s nanoscale distribution pattern. Finally, by incorporating the resulting annular tribocharge into electrohydrodynamic lithography, we also accomplish facile realization of nanovolcanos with 10 nm-scale craters.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Rooftop Energy Potential of Low Income Communities in America REPLICA

The Rooftop Energy Potential of Low Income Communities in America REPLICA data set provides estimates of residential rooftop solar technical potential at the tract-level with emphasis on estimates for Low and Moderate Income LMI populations. In addition to technical potential REPLICA is comprised of 10 additional datasets at the tract-level to provide socio-demographic and market context. The model year vintage of REPLICA is 2015. The LMI solar potential estimates are made at the tract level grouped by Area Median Income AMI income tenure and building type. These estimates are based off of LiDAR data of 128 metropolitan areas statistical modeling and ACS 2011-2015 demographic data. The remaining datasets are supplemental datasets that can be used in conjunction with the technical potential data for general LMI solar analysis planning and policy making. The core dataset is a wide-format CSV file seeds_ii_replica.csv that can be tagged to a tract geometry using the GEOID or GISJOIN fields. In addition users can download geographic shapefiles for the main or supplemental datasets. This dataset was generated as part of the larger NREL-led SEEDSII Solar Energy Evolution and Diffusion Studies project and specifically for the NREL technical report titled Rooftop Solar Technical Potential for Low-to-Moderate Income Households in the United States by Sigrin and Mooney 2018. This dataset is intended to give researchers planners advocates and policy-makers access to credible data to analyze low-income solar issues and potentially perform cost-benefit analysis for program design. To explore the data in an interactive web mapping environment use the NREL SolarForAll app.

14 SOLAR ENERGY↗

B-DeepONet: An enhanced Bayesian DeepONet for solving noisy parametric PDEs using accelerated replica exchange SGLD

Here, the Deep Operator Network (DeepONet) is a neural network architecture used to approximate operators, including the solution operator of parametric PDEs. DeepONets have shown remarkable approximation ability. However, the performance of DeepONets deteriorates when the training data is polluted with noise, a scenario that occurs in practice. To handle noisy data, we propose a Bayesian DeepONet based on replica exchange Langevin diffusion (reLD). Replica exchange uses two particles. The first particle trains a DeepONet to exploit the loss landscape and make predictions. The other particle trains a different DeepONet to explore the loss landscape and escape local minima via swapping. Compared to DeepONets trained with state-of-the-art gradient-based algorithms (e.g., Adam), the proposed Bayesian DeepONet greatly improves the training convergence for noisy scenarios and accurately estimates the uncertainty. To further reduce the high computational cost of the reLD training of DeepONets, we propose (1) an accelerated training framework that exploits the DeepONet's architecture to reduce its computational cost up to 25% without compromising performance and (2) a transfer learning strategy that accelerates training DeepONets for PDEs with different parameter values. Finally, we illustrate the effectiveness of the proposed Bayesian DeepONet using four parametric PDE problems.

97 MATHEMATICS AND COMPUTING↗

Multiply accelerated ReaxFF molecular dynamics: coupling parallel replica dynamics with collective variable hyper dynamics

To address the time scales required to study complex chemical reactions, methods performing accelerated molecular dynamics are necessary even with the recent advancement in high-performance computing. A number of different acceleration techniques are available. Here we explore potential synergies between two popular acceleration methods – Parallel Replica Dynamics (PRD) and Collective Variable Hyperdynamics (CVHD), by analysing the speedup obtained for the pyrolysis of n-dodecane. We determine that PRD + CVHD provides additional speedup to CVHD by reaching the required time scales for the reaction at an earlier wall-clock time. Although some speedup is obtained with the additional replicas, we found that the effectiveness of the inclusion of PRD is depreciated for systems where there is a dramatic increase in reaction rates induced by CVHD. Similar observations were made in the simulation of ethylene-carbonate/Li system, which is inherently more reactive than pyrolysis, suggest that the speedup obtained via the combination of the two acceleration methods can be generalised to most practical chemical systems.

42 ENGINEERING↗

Atomic-scale mechanism of carbon nucleation from a deep crustal fluid by replica exchange reactive molecular dynamics simulation

Here we present a mechanistic model of carbon nucleation and growth from a fluid at elevated temperature (T) and pressure conditions, typical of those found in the shallow Earth’s lithosphere. Our model uses a replica exchange reactive molecular dynamics framework in which molecular configurations are swapped between adjacent T replica at regular intervals according to underlying statistical mechanics. This framework allows predicting complex molecular structures and thermodynamics while remaining computationally efficient. Here we simulate the reactivity of an unstable mixture of CO 2 and CH 4 at 1000 K and 1 GPa. We find that the path to thermodynamic equilibrium is initially entropy-driven, producing a diversity of short-lived species, including various alcohols with intermediate carbon oxidation states. Cyclic and polycyclic radicals that are sometimes resonance-stabilized form next and set the stage for carbon nucleation. The carbon exsolution process releases abundant water, is exothermic and starts with the nucleation of a large aggregate of hydrogenated graphene flakes from covalently bonded polycyclic units. The carbon backbone of this nucleus subsequently grows into a hydrogen-depleted fullerene-like structure, before evolving toward a partially bilayered graphene layer. Overall, our results show that the mechanism of graphitic C formation is certainly not bimolecular, and that it may involve a combination of key condensation and radical chain reactions. This will help understand the isotopic, and reactive characteristics of carbon-bearing fluids during their upward transit through the Earth’s mantle and crust. Moreover, the mechanistic insights outlined here present intriguing similarities with the process of soot and interstellar dust formation, which suggests that the widespread distribution of abiotic polyaromatic and graphitic material on Earth and beyond may reflect the prevalence of a fundamental chemical pathway.

58 GEOSCIENCES↗