Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) has enabled modeling macromolecular complexes that are essential components of life. The density maps obtained from cryo-EM experiments is often integrated with ab-initio, knowledge-driven or first principles-based computational methods to build, fit and refine protein structures inside the electron density maps. Going beyond a single stationary-structure determination scheme, it is becoming more common to interpret the experimental data with a set of multiple physical models all of which contributes to the average observation seen by the experiment. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. In this work, we demonstrate such adaptive decision making capabilities during flexible fitting of biomolecules. Our solution uses RADICAL tools (RCT) and we test this new implementation in exascale high performance computing environment for two proteins, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). Our results indicate that using multiple replicas in flexible fitting with adaptive decision making improves the overall quality of fit and model by 40 % improvement when compared against the traditional flexible fitting approach. These advances are agnostic to system-size and computing environments.

Magnetopause ripples going against the flow form azimuthally stationary surface waves

Surface waves process the turbulent disturbances which drive dynamics in many space, astrophysical and laboratory plasma systems, with the outer boundary of Earth’s magnetosphere, the magnetopause, providing an accessible environment to study them. Like waves on water, magnetopause surface waves are thought to travel in the direction of the driving solar wind, hence a paradigm in global magnetospheric dynamics of tailward propagation has been well-established. Here we show through multi-spacecraft observations, global simulations, and analytic theory that the lowest-frequency impulsively-excited magnetopause surface waves, with standing structure along the terrestrial magnetic field, propagate against the flow outside the boundary. Across a wide local time range (09–15h) the waves’ Poynting flux exactly balances the flow’s advective effect, leading to no net energy flux and thus stationary structure across the field also. Further down the equatorial flanks, however, advection dominates hence the waves travel downtail, seeding fluctuations at the resonant frequency which subsequently grow in amplitude via the Kelvin-Helmholtz instability and couple to magnetospheric body waves. This global response, contrary to the accepted paradigm, has implications on radiation belt, ionospheric, and auroral dynamics and potential applications to other dynamical systems.

Modeling th dynamics of charged drop of one liquid in another under the action of an electric field

The work is devoted to the study of the features of the behavior of a group of droplets of one viscous liquid in another under the influence of various physical fields. When considering the dynamics of two drops under the action of an electric field, it is assumed that a drop in the form of a sphere with radius а will be placed in an electric field with an intensity , investigates how droplets will react to each other under the influence of an electric field. A mathematical model has been built and a computer program has been developed for the numerical solution of this problem. The behavior of several drops in an electric field is studied for different physical parameters of the material of the drops and the environment, as well as for different initial distributions of drops and the strength of the electric field. It is shown for the first time that emulsion droplets distributed in space, under the action of an electric field, begin to move and after a certain time a new stationary structure of droplets is formed. It was found that the relaxation time depends on the electric field strength, the size of the droplets and their initial distribution.

Analysis of the trunk oil pipeline survivability in the zone of the butt welded joint

The article describes the development of a technique for analyzing the survivability of the trunk pipeline in the zone of the transverse weld during operation, taking into account the residual welding stresses. The calculation of residual welding stresses was performed by solving the problem of thermoelasto-viscoplasticity for a material with a non-stationary structure by the finite element method. Solving the nonlinear nonstationary heat conduction problem was carried out by the finite difference method using boundary conditions of the third kind. Modeling the kinetics of transformation of austenite into ferrite-pearlite and bainite under non-isothermal conditions during welding was carried out on the basis of the theory of isokinetic reactions. The calculation of survivability is based on the Irwin criterion and the Paris formula.

Evolution of nonlinear stationary formations in a quantum plasma at finite temperature

In this paper we have studied the gradual evolution of stationary formations in electron acoustic waves at a finite temperature quantum plasma. We have made use of Quantum hydrodynamics model equations and obtained the KdV-Burgers equation. From here we showed how the amplitude modulated solitons evolve from double layer structures through shock fronts and ultimately converging into solitary structures. We have studied the various parametric influences on such stationary structure and also showed how the gradual variations of these parameter affect the transition from one form to another. The results thus obtained will help in the generation and structure of the structures in their respective domain. Much of the experiments on dense plasma will benefit from the parametric study. Further we have studied amplitude modulation followed by a detailed study on chaos.

Long -term growth sources for sectors of Russian economy

Theoretical models suggest stationary structure of sectors. Sometimes this suggestion is hidden (balanced growth). The ratio of variables for 2 sectors is unit root at the most cases (for 14 Russian sectors and 6 variables per sector). The lowest share of stationary ratios is 5/91 for real value added with ADF test (KPSS test for the same variable leads to 38/91 stationary ratios). The cointegration rank differs across sectors in wide ranges (from 1 for trade (G) or government administration (L) till 5 for agriculture (AB)). The dynamic stochastic partial equilibrium (DSPE) model is created. It is model of firms in DSGE-style and description of the rest economy by exogenous rules. The model is estimated for each of 14 sectors. The model includes 5 sources of stochastic trends: TFP; labor supply; investments efficiency; investments prices; prices of intermediate goods. Any 2 sectors significantly differ by key parameters (production function shares, capital depreciation, and demand elasticity). The drift of unit root sources differs across sectors (including sign). Only few pairs of sectors differ insignificantly (3/182 or 8/91 depending on test specification). The variance decomposition of trends (for various variables) is computed. It varies in wide ranges across sectors and variables. Thus, usage of aggregate data in theoretical model leads to loose of large amount of information.

Estimating survival in echinoid populations

Estimating survival rate is a basic part of population studies. Generally it is assumed that populations being studied are both stable and stationary. This probably is seldom the case although as a long-term average populations may persist at a mean density. Estimating survival in short-term studies may fail to capture average rates. A long-term study of the purple sea urchin Strongylocentrotus purpuratus at Sunset Bay, OR, USA from 1964–2009 is used to demonstrate methods for estimating survival based on the coefficient of variation of size distributions, the fraction of new recruits in a population, means of size data coupled with estimates of growth, and a method that uses rates of flow through size categories. A short-term study of just a few years may by chance sample when an unusual recruitment event drives a population far from stationary structure and so distorts the estimate of mean survival. The best solution, as shown for S. purpuratus, is a long time series but in advance it cannot be determined how long this should be. If a study of three years shows no substantial change in population size structure it may be reasonable to accept estimates of survival.

Condition monitoring for airport baggage handling in the era of industry 4.0

Purpose The purpose of this paper is to present the findings of a recent study conducted with the objective of addressing the problem of failure of baggage carts in the high-speed baggage tunnel at Heathrow Terminal 5 by the development of an innovative condition-based maintenance system designed to meet the requirements of twenty-first century airport systems and Industry 4.0. Design/methodology/approach An empirical experimental approach to this action research was taken to install a vibration condition monitoring pilot test in the north tunnel at Terminal 5. Vibration data were collected over a 6-month period and analysed to find the threshold of good quality tires and those with worn bearings that needed replacement. The results were compared with existing measures to demonstrate that vibration monitoring could be used as a predictive model for condition-based maintenance. Findings The findings demonstrated a clear trend of increasing vibration velocity with age and use of the baggage cart wheels caused by wheel mass unbalanced inertia that was transmitted to the tracks as vibration. As a result, preventative maintenance is essential to ensure the smooth running of airport baggage. This research demonstrates that a healthy wheel produces vibration of under 60 mm/s whereas a damaged wheel measures up to 100 mm/s peak-to-peak velocity and this can be used in real-time condition monitoring to prevent baggage cart failure. It can also run as an autonomous system linked to AI and Industry 4.0 airport logic. Originality/value Whilst vibration monitoring has been used to measure movement in static structures such as bridges and used in rotating machinery such as railway wheels (Tondon and Choudhury, 1999) this is unique as it is the first time it has been applied on a stationary structure (tracks) carrying high-speed rotating machinery (baggage cart wheels). This technique has been patented and proven in the pilot study and is in the process of being rolled out to all Heathrow terminal connection tunnels. It has implications for all other airports world-wide and, with new economic sensors, to other applications that rely on moving conveyor belts.

Stability of shock wave structures in nonlinear elastic media

The stationary structure stability of discontinuous solutions to nonlinear hyperbolic equations describing the propagation of quasi-transverse waves with velocities close to characteristic ones are studied. A procedure to analyze spectral (linear) stability of these solutions is described. The main focus is the stability analysis of special discontinuities, the stationary structure of which is represented by the integral curve connecting two saddle points corresponding to the states in front of and behind the discontinuity. This analysis is done using the properties of the Evans function, an analytic function on the right complex half-plane, which has zeros in this domain if and only if there exist unstable modes of linearization around a solution representing a special discontinuity with the structure.

Innovative airport 4.0 condition-based maintenance system for baggage handling DCV systems

PurposeThe purpose of this paper is to present the findings of a recent study conducted with the objective of addressing the problem of failure of baggage carts in the high-speed baggage tunnel at Heathrow Terminal 5 by the development of an innovative condition-based maintenance (CBM) system designed to meet the requirements of 21st century airport systems and Industry 4.0.Design/methodology/approachAn empirical experimental approach to this action research was taken to install a vibration condition monitoring pilot test in the north tunnel at Terminal 5. Vibration data were collected over a 6-month period and analysed to find the threshold of good quality tyres and those with worn bearings that needed replacement. The results were compared with existing measures to demonstrate that vibration monitoring could be used as a predictive model for CBM.FindingsThe findings demonstrated a clear trend of increasing vibration velocity with age and use of the baggage cart wheels caused by wheel mass unbalanced inertia that was transmitted to the tracks as vibration. As a result, preventative maintenance is essential to ensure the smooth running of airport baggage. This research demonstrates that a healthy wheel produces vibration of under 60 mm/s whereas a damaged wheel measures up to 100 mm/s peak to peak velocity and this can be used in real-time condition monitoring to prevent baggage cart failure. It can also run as an autonomous system linked to AI and Industry 4.0 airport logic.Originality/valueWhilst vibration monitoring has been used to measure movement in static structures such as bridges and used in rotating machinery such as railway wheels (Tondon and Choudhury, 1999); this is unique as it is the first time it has been applied on a stationary structure (tracks) carrying high-speed rotating machinery (baggage cart wheels). This technique has been patented and proven in the pilot study and is in the process of being rolled out to all Heathrow terminal connection tunnels. It has implications for all other airports worldwide and, with new economic sensors, to other applications that rely on moving conveyor belts.