Ground Based Program for the Physical Analysis of Macromolecular Crystal Growth

During the past year we have focused on application of in situ Atomic Force Microscopy (AFM) for studies of the growth mechanisms and kinetics of crystallization for different macromolecular systems. Mechanisms of macrostep formation and their decay, which are important in understanding of defect formation, were studied on the surfaces of thaumatin, catalase, canavalin and lysozyme crystals. Experiments revealed that step bunching on crystalline surfaces occurred either due to two- or three-dimensional nucleation on the terraces of vicinal slopes or as a result of uneven step generation by complex dislocation sources. No step bunching arising from interaction of individual steps in the course of the experiment was observed. The molecular structure of the growth steps for thaumatin and lipase crystals were deduced. It was further shown that growth step advance occurs by incorporation of single protein molecules. In singular directions growth steps move by one-dimensional nucleation on step edges followed by lateral growth. One-dimensional nuclei have different sizes, less then a single unit cell, varying for different directions of step movement. There is no roughness due to thermal fluctuations, and each protein molecule which incorporated into the step remained. Growth kinetics for catalase crystals was investigated over wide supersaturation ranges. Strong directional kinetic anisotropy in the tangential step growth rates in different directions was seen. The influence of impurities on growth kinetics and cessation of macromolecular crystals was studied. Thus, for catalase, in addition to pronounced impurity effects on the kinetics of crystallization, we were also able to directly observe adsorption of some impurities. At low supersaturation we repeatedly observed filaments which formed from impurity molecules sedimenting on the surfaces. Similar filaments were observed on the surfaces of thaumatin, canavalin and STMV crystals as well, but the frequency was low compared with catalase crystallization. Cessation of growth of xylanase and lysozyme crystals was also observed and appeared to be a consequence of the formation of dense impurity adsorption layers. Attachment: "An in situ AFM investigation of catalase crystallization", "Atomic force microscopy studies of living cells: visualization of motility, division, aggregation, transformation, and apoptosis", AFM studies on mechanisms of nucleation and growth of macromolecular crystals", and "In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization"

X-ray diffraction and atomic force microscopy analysis of twinned crystals: rhombohedral canavalin

The structure of canavalin, the vicilin-class storage protein from jack bean, was refined to 1.7 A resolution in a highly twinned rhombohedral crystal of space group R3 and unit-cell parameters a = b = c = 83.0 A, alpha = beta = gamma = 111.1 degrees. The resulting R and R(free) were 0.176 and 0.245, respectively. The orthorhombic crystal structure (space group C222(1), unit-cell parameters a = 136.5, b = 150.3, c = 133.4 A) was also refined with threefold non-crystallographic symmetry restraints. R and R(free) were 0.181 and 0.226, respectively, for 2.6 A resolution data. No significant difference in the protein structure was seen between these two crystal forms, nor between these two and the hexagonal and cubic crystal forms reported elsewhere [Ko et al. (1993), Acta Cryst. D49, 478-489; Ko et al. (1993), Plant Physiol. 101, 729-744]. A phosphate ion was identified in the lumen of the C-terminal beta-barrel. Lattice interactions showed that the trimeric molecule could be well accommodated in both 'top-up' and 'bottom-up' orientations in a rhombohedral unit cell of the R3 crystal and explained the presence of a high twin fraction. The large inter-trimer stacking interface of the C222(1) crystal may account for its relative stability. Atomic force microscopy (AFM) investigations of the growth of three crystal forms of canavalin indicate the rhombohedral form to be unique. Unlike the other two crystal forms, it contains at least an order of magnitude more screw dislocations and stacking faults than any other macromolecular crystal yet studied, and it alone grows principally by generation of steps from the screw dislocations. The unusually high occurrence of the screw dislocations and stacking faults is attributed to mechanical stress produced by the alternate molecular orientations in the rhombohedral crystals and their organization into discrete domains or blocks. At boundaries of alternate domains, lattice strain is relieved by the formation of the screw dislocations

Таємниця одного адміністратора

Провінційний чиновник, особливо дореформених часів, – і досі рідкісний гість на сторінках вітчизняних наукових монографій, дисертаційних досліджень, ба, навіть, статей у спеціалізованих періодичних виданнях. Поясненням цього феномену є, мабуть, сформована ще класичною російською літературою і діяча-ми доби Великих Реформ слава більшості миколаївських чиновників чи то як «сірості», посередності (стор. 73), чи то як хабарників і крадіїв [1]. З іншого боку, тривалій відразі до студій з адміністративної історії прислужилася логіка т.зв. «національного наративу», за якою місцевий представник імперської адміністра-ції видавався своєрідним «чужинцем» – колоніалістом чи колабораціоністом. Втім, останні десять років досі так само національно орієнтовані англо- і російськомовна історіографії демонструють тенденцію до «імперського пово-роту» («imperial turn»), зокрема, актуалізуючи і переосмислюючи проблематику адміністрування Російської імперії [2]. Вкупі зі зростаючою від часів Великих Реформ кількістю поодиноких праць із історії місцевого управління [3], зокре-ма, і біографічного спрямування [4], це дозволяє очікувати і вітчизняного рене-сансу студій у царині адміністративної історії

Employing combination procedures to short-time EOP prediction

A well known problem with Earth Orientation Parameters (EOP) prediction is that a prediction strategy proved to be the best for some testing time span and prediction length may not remain the same for other time intervals. In this paper, we consider possible strategies to combine EOP predictions computed using different analysis techniques to obtain a final prediction with the best accuracy corresponding to the smallest prediction error of input predictions. It was found that this approach is most efficient for ultra-short-term EOP forecast.Comment: 7 pages, presented at the IERS Workshop on EOP Combination and Prediction, Warsaw, Poland, 19-21 Oct 200

Project Achoo: A Practical Model and Application for COVID-19 Detection from Recordings of Breath, Voice, and Cough

The COVID-19 pandemic created a significant interest and demand for infection detection and monitoring solutions. In this paper we propose a machine learning method to quickly triage COVID-19 using recordings made on consumer devices. The approach combines signal processing methods with fine-tuned deep learning networks and provides methods for signal denoising, cough detection and classification. We have also developed and deployed a mobile application that uses symptoms checker together with voice, breath and cough signals to detect COVID-19 infection. The application showed robust performance on both open sourced datasets and on the noisy data collected during beta testing by the end users

Structure of orthorhombic crystals of beef liver catalase

The growth mechanisms and physical properties of the orthorhombic crystal form of beef liver catalase were investigated using in situ atomic force microscopy (AFM). It was observed that the crystals grow in the <001> direction by an unusual progression of sequential two-dimensional nuclei of half unit-cell layers corresponding to the 'bottoms' and 'tops' of unit cells. These were easily discriminated by their alternating asymmetric shapes and their strong growth-rate anisotropy. This pattern has not previously been observed with other macromolecular crystals. Orthorhombic beef liver catalase crystals exhibit an extremely high defect density and incorporate great numbers of misoriented microcrystals, revealed intact by etching experiments, which may explain their marginal diffraction properties. To facilitate interpretation of AFM results in terms of intermolecular interactions, the structure of the orthorhombic crystals, having an entire tetramer of the enzyme as the asymmetric unit, was solved by molecular replacement using a model derived from a trigonal crystal form. It was subsequently refined by conventional techniques. Although the packing of molecules in the two unit cells was substantially different, with very few exceptions no significant differences in the molecular structures were observed. In addition, no statistically significant deviation from ideal 222 molecular symmetry appeared within the tetramer. The packing of molecules in the crystal revealed by X-ray analysis explained in a satisfying way the process of crystal growth revealed by AFM

Nonequilibrium orientational patterns in two-component Langmuir monolayers

A model of a phase-separating two-component Langmuir monolayer in the presence of a photo-induced reaction interconvering two components is formulated. An interplay between phase separation, orientational ordering and treaction is found to lead to a variety of nonequilibrium self-organized patterns, both stationary and traveling. Examples of the patterns, observed in numerical simulations, include flowing droplets, traveling stripes, wave sources and vortex defects.Comment: Submitted to the Physical Review

Simulation-free Schr\"odinger bridges via score and flow matching

We present simulation-free score and flow matching ([SF]$^2$M), a simulation-free objective for inferring stochastic dynamics given unpaired source and target samples drawn from arbitrary distributions. Our method generalizes both the score-matching loss used in the training of diffusion models and the recently proposed flow matching loss used in the training of continuous normalizing flows. [SF]$^2$M interprets continuous-time stochastic generative modeling as a Schr\"odinger bridge (SB) problem. It relies on static entropy-regularized optimal transport, or a minibatch approximation, to efficiently learn the SB without simulating the learned stochastic process. We find that [SF]$^2$M is more efficient and gives more accurate solutions to the SB problem than simulation-based methods from prior work. Finally, we apply [SF]$^2$M to the problem of learning cell dynamics from snapshot data. Notably, [SF]$^2$M is the first method to accurately model cell dynamics in high dimensions and can recover known gene regulatory networks from simulated data.Comment: A version of this paper appeared in the New Frontiers in Learning, Control, and Dynamical Systems workshop at ICML 2023. Code: https://github.com/atong01/conditional-flow-matchin