Holographic single particle imaging for weakly scattering, heterogeneous nanoscale objects

Single particle imaging (SPI) at X-ray free electron lasers (XFELs) is a technique to determine the 3D structure of nanoscale objects like biomolecules from a large number of diffraction patterns of copies of these objects in random orientations. Millions of low signal-to-noise diffraction patterns with unknown orientation are collected during an X-ray SPI experiment. The patterns are then analyzed and merged using a reconstruction algorithm to retrieve the full 3D-structure of particle. The resolution of reconstruction is limited by background noise, signal-to-noise ratio in diffraction patterns and total amount of data collected. We recently introduced a reference-enhanced holographic single particle imaging methodology [Optica 7,593-601(2020)] to collect high enough signal-to-noise and background tolerant patterns and a reconstruction algorithm to recover missing parameters beyond orientation and then directly retrieve the full Fourier model of the sample of interest. Here we describe a phase retrieval algorithm based on maximum likelihood estimation using pattern search dubbed as MaxLP, with better scalability for fine sampling of latent parameters and much better performance in the low signal limit. Furthermore, we show that structural variations within the target particle are averaged in real space, significantly improving robustness to conformational heterogeneity in comparison to conventional SPI. With these computational improvements, we believe reference-enhanced SPI is capable of reaching sub-nm resolution biomolecule imaging

Continuous Diffraction of Molecules and Disordered Molecular Crystals

The diffraction pattern of a single non-periodic compact object, such as a molecule, is continuous and is proportional to the square modulus of the Fourier transform of that object. When arrayed in a crystal, the coherent sum of the continuous diffracted wave-fields from all objects gives rise to strong Bragg peaks that modulate the single-object transform. Wilson statistics describe the distribution of continuous diffraction intensities to the same extent that they apply to Bragg diffraction. The continuous diffraction obtained from translationally-disordered molecular crystals consists of the incoherent sum of the wave-fields from the individual rigid units (such as molecules) in the crystal, which is proportional to the incoherent sum of the diffraction from the rigid units in each of their crystallographic orientations. This sum over orientations modifies the statistics in a similar way that crystal twinning modifies the distribution of Bragg intensities. These statistics are applied to determine parameters of continuous diffraction such as its scaling, the beam coherence, and the number of independent wave-fields or object orientations contributing. Continuous diffraction is generally much weaker than Bragg diffraction and may be accompanied by a background that far exceeds the strength of the signal. Instead of just relying upon the smallest measured intensities to guide the subtraction of the background it is shown how all measured values can be utilised to estimate the background, noise, and signal, by employing a modified "noisy Wilson" distribution that explicitly includes the background. Parameters relating to the background and signal quantities can be estimated from the moments of the measured intensities. The analysis method is demonstrated on previously-published continuous diffraction data measured from imperfect crystals of photosystem II.Comment: 34 pages, 11 figures, 2 appendice

Possible Detection of Causality Violation in a Non-local Scalar Model

We consider the possibility that there may be causality violation detectable at higher energies. We take a scalar nonlocal theory containing a mass scale $\Lambda$ as a model example and make a preliminary study of how the causality violation can be observed. We show how to formulate an observable whose detection would signal causality violation. We study the range of energies (relative to $\Lambda$) and couplings to which the observable can be used.Comment: Latex, 30 page

Matrix product solution to an inhomogeneous multi-species TASEP

We study a multi-species exclusion process with inhomogeneous hopping rates. This model is equivalent to a Markov chain on the symmetric group that corresponds to a random walk in the affine braid arrangement. We find a matrix product representation for the stationary state of this model. We also show that it is equivalent to a graphical construction proposed by Ayyer and Linusson, which generalizes Ferrari and Martin's construction

Remarks on the multi-species exclusion process with reflective boundaries

We investigate one of the simplest multi-species generalizations of the one dimensional exclusion process with reflective boundaries. The Markov matrix governing the dynamics of the system splits into blocks (sectors) specified by the number of particles of each kind. We find matrices connecting the blocks in a matrix product form. The procedure (generalized matrix ansatz) to verify that a matrix intertwines blocks of the Markov matrix was introduced in the periodic boundary condition, which starts with a local relation [Arita et al, J. Phys. A 44, 335004 (2011)]. The solution to this relation for the reflective boundary condition is much simpler than that for the periodic boundary condition

Phase diagram of a generalized ABC model on the interval

We study the equilibrium phase diagram of a generalized ABC model on an interval of the one-dimensional lattice: each site $i=1,...,N$ is occupied by a particle of type \a=A,B,C, with the average density of each particle species N_\a/N=r_\a fixed. These particles interact via a mean field non-reflection-symmetric pair interaction. The interaction need not be invariant under cyclic permutation of the particle species as in the standard ABC model studied earlier. We prove in some cases and conjecture in others that the scaled infinite system N\rw\infty, i/N\rw x\in[0,1] has a unique density profile \p_\a(x) except for some special values of the r_\a for which the system undergoes a second order phase transition from a uniform to a nonuniform periodic profile at a critical temperature $T_c=3\sqrt{r_A r_B r_C}/2\pi$.Comment: 25 pages, 6 figure

On the dynamical behavior of the ABC model

We consider the ABC dynamics, with equal density of the three species, on the discrete ring with $N$ sites. In this case, the process is reversible with respect to a Gibbs measure with a mean field interaction that undergoes a second order phase transition. We analyze the relaxation time of the dynamics and show that at high temperature it grows at most as $N^2$ while it grows at least as $N^3$ at low temperature

A central limit theorem for time-dependent dynamical systems

The work [8] established memory loss in the time-dependent (non-random) case of uniformly expanding maps of the interval. Here we find conditions under which we have convergence to the normal distribution of the appropriately scaled Birkhoff-like partial sums of appropriate test functions. A substantial part of the problem is to ensure that the variances of the partial sums tend to infinity (cf. the zero-cohomology condition in the autonomous case). In fact, the present paper is the first one where non-random, i. e. specific examples are also found, which are not small perturbations of a given map. Our approach uses martingale approximation technique in the form of [9]

Transfer matrices for the totally asymmetric exclusion process

We consider the totally asymmetric simple exclusion process (TASEP) on a finite lattice with open boundaries. We show, using the recursive structure of the Markov matrix that encodes the dynamics, that there exist two transfer matrices $T_{L-1,L}$ and $\tilde{T}_{L-1,L}$ that intertwine the Markov matrices of consecutive system sizes: $\tilde{T}_{L-1,L}M_{L-1}=M_{L}T_{L-1,L}$. This semi-conjugation property of the dynamics provides an algebraic counterpart for the matrix-product representation of the steady state of the process.Comment: 7 page

Combinatorial Markov chains on linear extensions

We consider generalizations of Schuetzenberger's promotion operator on the set L of linear extensions of a finite poset of size n. This gives rise to a strongly connected graph on L. By assigning weights to the edges of the graph in two different ways, we study two Markov chains, both of which are irreducible. The stationary state of one gives rise to the uniform distribution, whereas the weights of the stationary state of the other has a nice product formula. This generalizes results by Hendricks on the Tsetlin library, which corresponds to the case when the poset is the anti-chain and hence L=S_n is the full symmetric group. We also provide explicit eigenvalues of the transition matrix in general when the poset is a rooted forest. This is shown by proving that the associated monoid is R-trivial and then using Steinberg's extension of Brown's theory for Markov chains on left regular bands to R-trivial monoids.Comment: 35 pages, more examples of promotion, rephrased the main theorems in terms of discrete time Markov chain