Classification, inference and segmentation of anomalous diffusion with recurrent neural networks

Countless systems in biology, physics, and finance undergo diffusive dynamics. Many of these systems, including biomolecules inside cells, active matter systems and foraging animals, exhibit anomalous dynamics where the growth of the mean squared displacement with time follows a power law with an exponent that deviates from 1. When studying time series recording the evolution of these systems, it is crucial to precisely measure the anomalous exponent and confidently identify the mechanisms responsible for anomalous diffusion. These tasks can be overwhelmingly difficult when only few short trajectories are available, a situation that is common in the study of non-equilibrium and living systems. Here, we present a data-driven method to analyze single anomalous diffusion trajectories employing recurrent neural networks, which we name RANDI. We show that our method can successfully infer the anomalous exponent, identify the type of anomalous diffusion process, and segment the trajectories of systems switching between different behaviors. We benchmark our performance against the state-of-the art techniques for the study of single short trajectories that participated in the Anomalous Diffusion (AnDi) challenge. Our method proved to be the most versatile method, being the only one to consistently rank in the top 3 for all tasks proposed in the AnDi challenge

Better Stability with Measurement Errors

Often it is desirable to stabilize a system around an optimal state. This can be effectively accomplished using feedback control, where the system deviation from the desired state is measured in order to determine the magnitude of the restoring force to be applied. Contrary to conventional wisdom, i.e. that a more precise measurement is expected to improve the system stability, here we demonstrate that a certain degree of measurement error can improve the system stability. We exemplify the implications of this finding with numerical examples drawn from various fields, such as the operation of a temperature controller, the confinement of a microscopic particle, the localization of a target by a microswimmer, and the control of a population. © 2016, Springer Science+Business Media New York

In-situ measurements of the optical absorption of dioxythiophene-based conjugated polymers

Conjugated polymers can be reversibly doped by electrochemical means. This doping introduces new sub-bandgap optical absorption bands in the polymer while decreasing the bandgap absorption. To study this behavior, we have prepared an electrochemical cell allowing measurements of the optical properties of the polymer. The cell consists of a thin polymer film deposited on gold-coated Mylar behind which is another polymer that serves as a counterelectrode. An infrared transparent window protects the upper polymer from ambient air. By adding a gel electrolyte and making electrical connections to the polymer-on-gold films, one may study electrochromism in a wide spectral range. As the cell voltage (the potential difference between the two electrodes) changes, the doping level of the conjugated polymer films is changed reversibly. Our experiments address electrochromism in poly(3,4-ethylene-dioxy-thiophene) (PEDOT) and poly(3,4-dimethyl-propylene-dioxy-thiophene) (PProDOT-Me$_2$). This closed electrochemical cell allows the study of the doping induced sub-bandgap features (polaronic and bipolaronic modes) in these easily oxidized and highly redox switchable polymers. We also study the changes in cell spectra as a function of polymer thickness and investigate strategies to obtain cleaner spectra, minimizing the contributions of water and gel electrolyte features

Enhanced force-field calibration via machine learning

The influence of microscopic force fields on the motion of Brownian particles plays a fundamental role in a broad range of fields, including soft matter, biophysics, and active matter. Often, the experimental calibration of these force fields relies on the analysis of the trajectories of the Brownian particles. However, such an analysis is not always straightforward, especially if the underlying force fields are non-conservative or time-varying, driving the system out of thermodynamic equilibrium. Here, we introduce a toolbox to calibrate microscopic force fields by analyzing the trajectories of a Brownian particle using machine learning, namely, recurrent neural networks. We demonstrate that this machine-learning approach outperforms standard methods when characterizing the force fields generated by harmonic potentials if the available data are limited. More importantly, it provides a tool to calibrate force fields in situations for which there are no standard methods, such as non-conservative and time-varying force fields. In order to make this method readily available for other users, we provide a Python software package named DeepCalib, which can be easily personalized and optimized for specific force fields and applications. This package is ideal to calibrate complex and non-standard force fields from short trajectories, for which advanced specific methods would need to be developed on a case-by-case basis

KORONER ARTER HASTALIĞININ BELİRLEYİCISI OLARAK PENIL DOPPLER ULTRASONOGRAFİ İLE SAPTANAN KAVERNOZ ARTER STENOZU: OLGU SUNUMU

An association between Coronary Artery Disease (CAD) and Erectile Dysfunction (ED) has been described. We aimed to show that cavernous artery stenosis may be an important predictor of a silent but serious CAD. A 56-year-old man who had moderate ED was evaluated for risk factors. He had several vascular risk factors for ED and CAD including age, smoking, hypertension, hyperhomocysteinemia and hyperlipidemia. His penile colour Doppler ultrasonography revealed multiple stenotic area in the right cavernous artery. His treadmill exercise test showed significant changes. Then, coronary angiography was performed and it showed the patient had doublevessel CAD. Findings of atherosclerotic plaques in cavernosal arteries with penile Doppler ultrasonography may be address subclinical coronary artery stenosis in patients with ED. Koroner arter hastalığı ile erektil disfonksiyon arasındaki ilişki belirgindir. Bu yazıda kavernozal arter darlığının sessiz fakat ciddi koroner arter hastalığını gösterebileceğinin ortaya konulması amaçlandı. Orta şiddette erektil disfonksiyon yakınması olan 56 yaşındaki hasta risk faktörleri açısından değerlendirildi. Hastanın yaş, sigara, hipertansiyon, hiperhomosisteinemi ve hiperlipidemi olmak üzere çok sayıda vasküler risk faktörü vardı. Penil Doppler ultrasonografide sağ kavernozal arterde çok sayıda darlık saptandı. Treadmill egzersiz testinde belirgin değişiklikleri olan hastanın yapılan koroner anjiografisinde iki damarda stenoz saptandı. Erektil disfonksiyonlu hastalarda penil Doppler ultrasonografi ile kavernozal arterlerde saptanan aterosklerotik plaklar subklinik koroner arter hastalığı habercisi olabilir

Financing profitability optimization: case study on sharia business unit of regional development banks in Indonesia

The study aims to examine the financing profitability optimization as recorded by Sharia Business Unit of Regional Development Banks (RDBs) in Indonesia. The profitability measured by Net Operating Margin (NOM) and predicted variables were tested with the ratio of Operational Cost to Operational Income (BOPO), Non-Performing Financing (NPF) and Profit Sharing Financing (PSF). On the basis of the literature review conducted, the study proposed five path coefficients to impact NOM, of which the constructed direct path to NOM was three and two for indirect paths. Time series data used were obtained from annual reports and publication reports. Using Pearson Correlation and Path Analysis, the study has found that BOPO, PSF, and NPF contributed to impact to NOM directly, and PSF impacted NOM indirectly through BOPO. Interestingly, PSF recorded a negative impact on NOM, suggesting inefficiency matters faced by SBU of RDBs not contributed from PSF. Another interesting finding, NPF was found insignificant to BOPO, indicating loan default is not a major matter for inefficiency issue, but could be a tight financing policy

XPS and water contact angle measurements on aged and corona-treated PP

Effects of corona treatment and aging on commercially produced corona discharged polypropylene (PP) films were followed via surface sensitive roughness analysis by atomic force microscopy (AFM), water contact angle (WCA), and X-ray photoelectron spectroscopic (XPS) measurements. Roughness analysis by AFM gave similar results for both untreated and corona-treated samples. The measured water contact angle decreased after corona treatment but increased with aging. XPS findings revealed that corona treatment caused an increase in the O-containing species on the surface of the films, but the measured O/C atomic ratio decreased with aging. The angle dependence of the observed XPS O/C atomic ratio further revealed that surface modifications by the corona treatment were buried into the polymer away from the surface as a function of aging. This is attributed to a surface rearrangement of the macromolecules in agreement with the findings of Garbassi et al. on oxygen-plasma-treated polypropylene

Non-Boltzmann stationary distributions and nonequilibrium relations in active baths

Most natural and engineered processes, such as biomolecular reactions, protein folding, and population dynamics, occur far from equilibrium and therefore cannot be treated within the framework of classical equilibrium thermodynamics. Here we experimentally study how some fundamental thermodynamic quantities and relations are affected by the presence of the nonequilibrium fluctuations associated with an active bath. We show in particular that, as the confinement of the particle increases, the stationary probability distribution of a Brownian particle confined within a harmonic potential becomes non-Boltzmann, featuring a transition from a Gaussian distribution to a heavy-tailed distribution. Because of this, nonequilibrium relations (e.g., the Jarzynski equality and Crooks fluctuation theorem) cannot be applied. We show that these relations can be restored by using the effective potential associated with the stationary probability distribution. We corroborate our experimental findings with theoretical arguments. © 2016 American Physical Society