In fully-inverted atomic ensembles, photon-mediated interactions give rise to Dicke superradiance, a form of many-body decay that results in a rapid release of energy as a photon burst. While originally studied in point-like ensembles, this phenomenon persists in extended ordered systems if the inter-particle distance is below a certain bound. Here, we investigate Dicke superradiance in a realistic experimental setting using ordered arrays of alkaline earth(-like) atoms, such as strontium and ytterbium. Such atoms offer exciting new opportunities for light-matter interaction as their internal structure offers the possibility of trapping at short interatomic distances compared to their strong long-wavelength transitions, providing the potential for strong collectively modified interactions. Despite their intricate electronic structure, we show that two-dimensional arrays of these atomic species should exhibit many-body superradiance for achievable lattice constants. Moreover, superradiance effectively ''closes'' transitions, such that multilevel atoms become more two-level like. This occurs because the avalanche-like decay funnels the emission of most photons into the dominant transition, overcoming the single-atom decay ratios dictated by their fine structure and Zeeman branching. Our work represents an important step in harnessing alkaline-earth atoms as quantum optical sources and as dissipative generators of entanglement.
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Long-Range Interactions for Hydrogen Atoms in Excited D States
Pressure shifts inside an atomic beam are among the more theoretically challenging effects in high-precision measurements of atomic transitions. A crucial element in their theoretical analysis is the understanding of long-range interatomic interactions inside the beam. For excited reference states, the presence of quasi-degenerate states leads to additional challenges, due to the necessity to diagonalize large matrices in the quasi-degenerate hyperfine manifolds. Here, we focus on the interactions of hydrogen atoms in reference states composed of an excited nD state (atom A), and in the metastable 2S state (atom B). We devote special attention to the cases n=3 and n=8. For n=3, the main effect is generated by quasi-degenerate virtual P states from both atoms A and B and leads to experimentally relevant second-order long-range (van-der-Waals) interactions proportional to the sixth inverse power of the interatomic distance. For n=8, in addition to virtual states with two states of P symmetry, one needs to take into account combined virtual P and F states from atoms A and B. The numerical value of the so-called C6 coefficients multiplying the interaction energy was found to grow with the principal quantum number of the reference D state; it was found to be of the order of 1011 in atomic units. The result allows for the calculation of the pressure shift inside atomic beams while driving transitions to nD states.
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- Award ID(s):
- 2110294
- NSF-PAR ID:
- 10330480
- Date Published:
- Journal Name:
- Atoms
- Volume:
- 10
- Issue:
- 1
- ISSN:
- 2218-2004
- Page Range / eLocation ID:
- 6
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract The electronic structure of magnetic lanthanide atoms is fascinating from a fundamental perspective. They have electrons in a submerged open 4f shell lying beneath a filled 6s shell with strong relativistic correlations leading to a large magnetic moment and large electronic orbital angular momentum. This large angular momentum leads to strong anisotropies, i. e. orientation dependencies, in their mutual interactions. The long-ranged molecular anisotropies are crucial for proposals to use ultracold lanthanide atoms in spin-based quantum computers, the realization of exotic states in correlated matter, and the simulation of orbitronics found in magnetic technologies. Short-ranged interactions and bond formation among these atomic species have thus far not been well characterized. Efficient relativistic computations are required. Here, for the first time we theoretically determine the electronic and ro-vibrational states of heavy homonuclear lanthanide Er 2 and Tm 2 molecules by applying state-of-the-art relativistic methods. In spite of the complexity of their internal structure, we were able to obtain reliable spin–orbit and correlation-induced splittings between the 91 Er 2 and 36 Tm 2 electronic potentials dissociating to two ground-state atoms. A tensor analysis allows us to expand the potentials between the atoms in terms of a sum of seven spin–spin tensor operators simplifying future research. The strengths of the tensor operators as functions of atom separation are presented and relationships among the strengths, derived from the dispersive long-range interactions, are explained. Finally, low-lying spectroscopically relevant ro-vibrational energy levels are computed with coupled-channels calculations and analyzed.more » « less
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This data set for the manuscript entitled "Design of Peptides that Fold and Self-Assemble on Graphite" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.
Version: 2.0
Changes versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.
Conventions Used in These Files
===============================Structure Files
----------------
- graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)
- repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)
- freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)
- amber_*.prmtop (combined topology and parameter files for Amber force field simulations)
- repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)Force Field Parameters
----------------------
CHARMM format parameter files:
- par_all36m_prot.prm (CHARMM36m FF for proteins)
- par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.
- toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)Template NAMD Configuration Files
---------------------------------
These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):
- template_min.namd (minimization)
- template_eq.namd (NPT equilibration with lower graphene fixed)
- template_abf.namd (for adaptive biasing force)Minimization
-------------
- namd/min_*.0.namdEquilibration
-------------
- namd/eq_*.0.namdAdaptive biasing force calculations
-----------------------------------
- namd/eabfZRest7_graph_chp1404.0.namd
- namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)Log Files
---------
For each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.Simulation Output
-----------------
The simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step = 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.Scripts
-------
Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.
CONTENTS
========The directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.
Sim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite–water interface.
Sim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite–water interface.
Sim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.
Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.
Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.
Sim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.
Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).
Sim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script ("doRestraintEnergyError.sh") in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.
Sim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene–water interface in the initial configuration.
Sim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.
Sim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite–water interface at 370 K.
Sim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.
This material is based upon work supported by the US National Science Foundation under grant no. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030. -
In this work we study a low-cost two-dimensional ferromagnetic semiconductor with possible applications in biomedicine, solar cells, spintronics, and energy and hydrogen storage. From first principle calculations we describe the unique electronic, transport, optical, and magnetic properties of a π-conjugated micropore polymer (CMP) with three iron atoms placed in the middle of an isolated pore locally resembling heme complexes. This material exhibits strong Fe-localized d z2 bands. The bandgap is direct and equal to 0.28 eV. The valence band is doubly degenerate at the Γ -point and for larger k -wavevectors the HOMO band becomes flat with low contribution to charge mobility. The absorption coefficient is roughly isotropic. The conductivity is also isotropic with the nonzero contribution in the energy range 0.3–8 eV. The xy -component of the imaginary part of the dielectric tensor determines the magneto-optical Faraday and Kerr rotation. Nonvanishing rotation is observed in the interval of 0.5–5.0 eV. This material is found to be a ferromagnet of an Ising type with long-range exchange interactions with a very high magnetic moment per unit cell, m = 6 μ B . The exchange integral is calculated by two independent methods: (a) from the energy difference between ferromagnetic and antiferromagnetic states and (b) from a magnon dispersion curve. In the former case J nn = 27 μeV. In the latter case the magnon dispersion is fitted by the Ising model with the nearest and next-nearest neighbor spin interactions. From these estimations we find that J nn = 19.5 μeV and J nnn = −3 μeV. Despite the different nature of the calculations, the exchange integrals are only within 28% difference.more » « less
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The high-pressure structure and stability of the calcic amphibole tremolite (Ca2Mg5Si8O22(OH)2) was investigated to ~40 GPa at 300 K by single-crystal X-ray diffraction using synchrotron radiation. C2/m symmetry tremolite displays a broader metastability range than previously studied clinoamphiboles, exhibiting no first-order phase transition up to 40 GPa. Axial parameter ratios a/b and a/c, in conjunction with finite strain versus normalized pressure trends, indicate that changes in compressional behavior occur at pressures of ~5 and ~20 GPa. An analysis of the finite strain trends, using third-order Birch-Murnaghan equations of state, resulted in bulk moduli (𝐾) of 72(7), 77(2), and 61(1) GPa for the compressional regimes from 0-5 GPa (regime I), 5-20 GPa (II), and above 20 GPa (III), respectively, and accompanying pressure-derivatives of the bulk moduli (𝐾′) of 8.6(42), 6.0(3), and 10.0(2). The results are consistent with first-principle theoretical calculations of tremolite elasticity. The axial compressibility ratios of tremolite, determined as 𝛽a : 𝛽b : 𝛽c = 2.22:1.0:0.78 (regime I), 2.12:1.0:0.96 (II), and 1.03:1.0:0.75 (III), demonstrate a substantial reduction of the compressional anisotropy of tremolite at high pressures, which is a notable contrast with the increasingly anisotropic compressibility observed in the high-pressure polymorphs of the clinoamphibole grunerite. The shift in compression-regime at 5 GPa (I-II) transition is ascribed to stiffening along the crystallographic a-axis corresponding to closure of the vacant A-site in the structure, and a shift in the topology of the a-oriented surfaces of the structural I-beam from concave to convex. The II-III regime shift at 20 GPa corresponds to an increasing rate of compaction of the Ca-polyhedra and increased distortion of the Mg-octahedral sites, processes which dictate compaction in both high-pressure compression-regimes. Bond-valence analyses of the tremolite structure under pressure show dramatic overbonding of the Ca-cations (75% at 30 GPa), with significant Mg-cation overbonding as well (40%). These imply that tremolite’s notable metastability range hinges on the calcium cation’s bonding environment. The 8-fold coordinated Ca-polyhedron accommodates significant compaction under pressure, while the geometry of the Ca-O polyhedron becomes increasingly regular and inhibits the reorientation of the tetrahedral chains that generate phase transitions observed in other clinoamphiboles. Peak/background ratio of diffraction data collected above 40 GPa and our equation of state determination of bulk moduli and compressibilities of tremolite in regime III, in concert with the results of our previous Raman study, suggest that C2/m tremolite may be approaching the limit of its metastability above 40 GPa. Our results have relevance for both the metastable compaction of tremolite during impact events, and for possible metastable persistence of tremolite within cold subduction zones within the Earth.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/atoms10010006
