本文以传播知识为目的，如有侵权请后台联系我们，我们将在第一时间删除。相干衍射成像（CDI）是一种无需透镜的成像技术，利用衍射的X射线、电子或可见光重建样品图像。CDI需要获取光子的相位和振幅，但通常只能恢复信号，不能保全相位信息，即相位丢失问题。![]()
Fig. 1 | Proposed PRAMMol method. 布拉格CDI可实现近原子分辨率，通过迭代相位恢复算法重建晶体三维应变场。现有相位恢复算法如误差减少和混合输入/输出等虽然有效，但常在局部最小值处停滞，面向原子分辨率的计算又变得更加昂贵，且可能难以收敛。此外，这些方法没有包含可能进一步约束解的物理信息。![]()
Fig. 2 |Asimulated FCC crystalline sample of 4679 atoms was created with atomsk with a single vacancy at the center.
结合密度泛函理论和分子动力学等材料模型的信息，有可能使解更加符合物理实际，显著缩小搜索空间。基于此，美国杨百翰大学物理与天文学系的Jason Meziere博士团队，提出了一种相位恢复算法，称为PRAMMol，即结合原子建模和分子动力学的相位恢复方法。Fig. 3 | Three peaks are simulated from the 6 nm sample with a single vacancy at its center.
该算法在求解过程中直接结合了物理模型，并在设计时考虑了衍射极限存储环同步辐射升级设计。这些同步加速器的升级将使相干X射线的亮度提升多达200倍，并可能实现亚埃分辨率。尽管相干电子源已有实例显示其达到原子分辨率，但CDI的原子分辨率却很难实现，仍具有挑战性。Fig. 4 | To evaluate the PRAMMol method, 10 trials were run across 20 values of TIPF, for a total of 200 trials.
由于升级后的同步辐射可能实现原子尺度的布拉格CDI运算，因此PRAMMol可设计用于原子尺度上的计算，并采用分子动力学作为物理模型（所有LAMMPS计算都是使用铝势能。不过作者坦诚该方法对具体势能不敏感，任何单原子间势能都可以获得类似结果）。相关论文近期发表于npj Computational Materials 10: 167 (2024).![]()
Fig. 5 | Reconstruction of sample with a vacancy takes a little more than 30 iterations to converge to the correct scaling constant and number of atoms.
Atomic resolution coherent x-ray imaging: Phase retrieval algorithm Coherent diffraction imaging (CDI) is a lensless imaging technique that
uses diffracted X-rays, electrons, or visible light to reconstruct images of
samples. CDI requires the retrieval of both the phase and amplitude of photons,
but typically only the signal can be recovered, leading to the phase problem.
Bragg CDI can achieve near-atomic resolution by reconstructing the
three-dimensional strain field of crystals using iterative phase retrieval
algorithms. Fig. 6 | Results of PRAMMol reconstructions of disjoint diffraction patterns with atomic resolution.
Existing phase retrieval algorithms, such as error reduction (ER)
and hybrid input-output (HIO), although effective, often get stuck in local
minima and do not incorporate material models. Integrating information from
material models like density functional theory and molecular dynamics can make
the solutions more physically accurate and significantly reduce the search
space.
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Fig. 7 | To assess the PRAMMol in experimental conditions, 10 trials were run accross 10 temperatures, for a total of 100 trials.
A team lead by Dr. Jason Meziere from Department of Physics &
Astronomy, Brigham Young University, USA, presented a
phase retrieval algorithm, called phase retrieval with atomic
modeling and molecular dynamics (PRAMMol). PRAMMol directly incorporates a physical model
during the solving process and was designed with expected diffraction limited
storage rings synchrotron upgrades in mind. These synchrotron upgrades
will allow for an increase of up to 200 times brightness in coherent x-rays,
and may enable sub-Ångstrom resolution. While atomic resolution has routinely
been demonstrated with coherent electron sources, atomic resolution from CDI
has been more challenging to achieve.
Fig. 8 | At 100 and 300 K, PRAMMol effectively reconstructs the entire object at atomic resolution except for a few locations on the surface.
Because upgraded synchrotrons could enable atomic scalein operando Bragg CDI, PRAMMol was designed to work at the atomic scale and uses MD as its physical model (All LAMMPS calculations are run with an Al potential. However, the
methodology presented here is agnostic to the specific potential used and any
monoatomic interatomic potential should achieve similar results). This article
was recently published in npj Computational Materials 10: 167 (2024).Fig. 9 | During cross validation, PRAMMol uses two lists of atomic positions, the atoms in the current object and new potential atom positions.
Atomic
resolution coherent x-ray imaging with physics-based phase retrieval (基于物理原理的相位恢复的原子级分辨率相干X射线成像)Jason Meziere, Abigail Hardy Carpenter, Anastasios Pateras, Ross Harder & Richard L. Sandberg
Abstract Coherent x-ray
imaging and scattering from accelerator based sources such as synchrotrons
continue to impact biology, medicine, technology, and materials science. Many
synchrotrons around the world are currently undergoing major upgrades to
increase their available coherent x-ray flux by approximately two orders of
magnitude. The improvement of synchrotrons may enable imaging of
materials in operando at the atomic scale which may
revolutionize battery and catalysis technologies. Current algorithms used for
phase retrieval in coherent x-ray imaging are based on the projection onto sets
method. These traditional iterative phase retrieval methods will become more
computationally expensive as they push towards atomic resolution and may
struggle to converge. Additionally, these methods do not incorporate physical
information that may additionally constrain the solution. In this work, we
present an algorithm which incorporates molecular dynamics into Bragg coherent
diffraction imaging (BCDI). This algorithm, which we call PRAMMol (Phase
Retrieval with Atomic Modeling and Molecular Dynamics) combines statistical
techniques with molecular dynamics to solve the phase retrieval problem. We
present several examples where our algorithm is applied to simulated coherent
diffraction from 3D crystals and show convergence to the correct solution at
the atomic scale.摘要 从加速器光源（如同步辐射）获取的相干X射线成像和散射，正持续对生物学、医学、技术和材料科学产生深远影响。目前，全球许多同步辐射加速器正在作大规模升级，想把相干X射线通量提升百倍。同步加速器的改进可能使我们能够在原子尺度上为材料成像，有可能彻底改变电池和催化技术。目前用于相干X射线成像的相位恢复算法主要基于投影集方法。这些传统迭代方法面向原子分辨率时显得更加昂贵，其计算可能难以收敛，而且尚未包含可能进一步约束解的物理信息。在这项工作中，我们提出了一种将分子动力学融入布拉格相干衍射成像的新算法。我们称这种算法为PRAMMol（结合原子建模和分子动力学的相位恢复），它结合了统计技术和分子动力学来解决相位恢复问题。我们展示了将该算法应用于模拟三维晶体的相干衍射的几个例子，并证明了该算法能够在原子尺度上成功收敛到正确解。
