Reservoir computing

I have developed an alternative numerical approach to study mass transfer from a stationary core-shell reservoir under channel flow conditions. I use the lattice Boltzmann method to compute both the solvent fluid flow and the diffusion and advection of the solute. I have investigated the impact of the flow by reporting mass transfer quantities such as the instantaneous solute concentration and the local Sherwood number at the surface of the reservoir. The flow is found to enhance the release of the encapsulated material, but it prevents the released material from reaching the channel walls...

For successful CO2 storage in underground reservoirs, the potential problem of CO2 leakage needs to be addressed. A profoundly improved understanding of the behavior of fractured cement under realistic subsurface conditions including elevated temperature, high pressure and the presence of CO2 saturated brine is required. Here, we report in-situ X-ray micro computed tomography (µ-CT) studies visualizing the micro-structural changes upon exposure of cured Portland cement with a leak path to CO2 saturated brine at high pressure...

Learning a task induces connectivity changes in neural circuits, thereby changing their dynamics. To elucidate task-related neural dynamics, we study trained recurrent neural networks. We develop a mean field theory for reservoir computing networks trained to have multiple fixed point attractors. Our main result is that the dynamics of the network's output in the vicinity of attractors is governed by a low-order linear ordinary differential equation. The stability of the resulting equation can be assessed, predicting training success or failure...

River flow is mainly controlled by climate, physiography and regulations, but their relative importance over large landmasses is poorly understood. Here we show from computational modelling that hydropower regulation is a key driver of flow regime change in snow-dominated regions and is more important than future climate changes. This implies that climate adaptation needs to include regulation schemes. The natural river regime in snowy regions has low flow when snow is stored and a pronounced peak flow when snow is melting...

Targeted inhibition of the oncogenic BCR-ABL1 fusion protein using the ABL1 tyrosine kinase inhibitor imatinib has become standard therapy for chronic myelogenous leukemia (CML), with most patients reaching total and durable remission. However, a significant fraction of patients develop resistance, commonly due to mutated ABL1 kinase domains. This motivated development of second-generation drugs with broadened or altered protein kinase selectivity profiles, including dasatinib and nilotinib. Imatinib-resistant patients undergoing treatment with second-line drugs typically develop resistance to them, but dynamic and clonal properties of this response differ...

Building proteins into larger, post-translational assemblies in a defined and stable way is still a challenging task. A promising approach relies on so-called tag/catcher systems that are fused to the proteins of interest and allow a durable linkage via covalent intermolecular bonds. Tags and catchers are generated by splitting protein domains that contain intramolecular isopeptide or ester bonds that form autocatalytically under physiological conditions. There are already numerous biotechnological and medical applications that demonstrate the usefulness of covalent linkages mediated by these systems...

In this study, the expected time required to eradicate HIV-1 completely was found as the conditional absorbing time in a finite state space continuous-time Markov chain model. The Markov chain has two absorbing states: one corresponds to HIV eradication and another representing the possible disaster. This method allowed us to calculate the expected eradication time by solving systems of linear equations. To overcome the challenge of huge dimension of the problem, we applied a novel stop and resume technique...

Nitric oxide is recognized as a signaling molecule involved in a broad range of physiological processes in plants including sexual reproduction. NO has been detected in the pollen grain at high levels and regulates pollen tube growth. Previous studies demonstrated that NO as well as ROS are produced in the olive reproductive tissues in a stage- and tissue-specific manner. The aim of this study was to assess the production of NO throughout the germination of olive (Olea europaea L.) pollen in vitro. The NO fluorescent probe DAF-2DA was used to image NO production in situ, which was correlated to pollen viability...

Memristive devices are promising circuit elements that enable novel computational approaches which go beyond the von-Neumann paradigms. Here by tuning the chemistry at the Al-LaNiO3 (LNO) interface, a metal-metal junction, we engineer good switching behavior with good electroresistance (ON-OFF resistance ratios of 100), and repeatable multiple resistance states. The active material responsible for such a behavior is a self-formed sandwich of an AlxOy layer at the interface obtained by grabbing oxygen by Al from LNO...

In forensic casework, non-invasive and minimally-invasive methods for postmortem examinations are extremely valuable. Whole body postmortem computed tomography (PMCT) is often used to provide visualization of the internal characteristics of a body prior to more invasive procedures and has also been used to locate gas reservoirs inside the body to assist in determining cause of death. Preliminary studies have demonstrated that exploiting the volatile organic compounds (VOCs) located in these gas reservoirs by comprehensive two-dimensional gas chromatography-high-resolution time-of-flight mass spectrometry (GC×GC-HRTOF-MS) may assist in providing information regarding the postmortem interval...

BACKGROUND: Late systolic load has been shown to cause diastolic dysfunction in animal models. Although the systolic loading sequence of the ventricular myocardium likely affects its coupling with the left atrium (LA), this issue has not been investigated in humans. We aimed to assess the relationship between the myocardial loading sequence and LA function in human hypertension. METHODS AND RESULTS: We studied 260 subjects with hypertension and 19 normotensive age- and sex-matched controls...

RNA viruses are one of the fastest evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus...

Our aim is to describe changes in the muscle-bone unit assessed as a ratio of bone mineral content (BMC) to lean body mass (LBM) through puberty at total body and various skeletal sites in Indian boys and girls. A cross-sectional study was conducted (888 children, 480 boys, aged 5-17 years) in Pune, India. Pubertal staging was assessed. BMC, LBM and fat percentage at the arms, legs, android, gynoid and total body (less the head) were assessed by dual energy X-ray absorptiometry. The amount of BMC per unit LBM (BMC/LBM) was computed...

Probiotic bacteria are known to harbor intrinsic and mobile genetic elements that confer resistance to a wide variety of antibiotics. Their high amounts in dietary supplements can establish a reservoir of antibiotic resistant genes in the human gut. These resistant genes can be transferred to pathogens that share the same intestinal habitat thus resulting in serious clinical ramifications. While antibiotic resistance of probiotic bacteria from food, human and animal sources have been well-documented, the resistant profiles of probiotics from dietary supplements have only been recently studied...

The practical application of microfluidic liver models for in vitro drug testing is partly hampered by their reliance on human primary hepatocytes, which are limited in number and have batch-to-batch variation. Human stem cell-derived hepatocytes offer an attractive alternative cell source, although their 3D differentiation and maturation in a microfluidic platform have not yet been demonstrated. We develop a pump-free microfluidic 3D perfusion platform to achieve long-term and efficient differentiation of human liver progenitor cells into hepatocyte-like cells (HLCs)...

Tight gas sandstone samples are imaged at high resolution industrial X-ray computed tomography (ICT) systems to provide a three-dimensional quantitative characterization of the fracture geometries. Fracture networks are quantitatively analyzed using a combination of 2-D slice analysis and 3-D visualization and counting. The core samples are firstly scanned to produce grayscale slices, and the corresponding fracture area, length, aperture and fracture porosity as well as fracture density were measured. Then the 2-D slices were stacked to create a complete 3-D image using volume-rendering software...

Reservoir computing is a recently introduced machine learning paradigm that has been shown to be well-suited for the processing of spatiotemporal data. Rather than training the network node connections and weights via backpropagation in traditional recurrent neural networks, reservoirs instead have fixed connections and weights among the 'hidden layer' nodes, and traditionally only the weights to the output layer of neurons are trained using linear regression. We claim that for signal classification tasks one may forgo the weight training step entirely and instead use a simple supervised clustering method based upon principal components of reservoir states...

Design of managed aquifer recharge (MAR) for augmentation of groundwater resources often lacks detailed data, and simple diagnostic tools for evaluation of the water table in a broad range of parameters are needed. In many large-scale MAR projects, the effect of a regional aquifer base dip cannot be ignored due to the scale of recharge sources (e.g., wadis, streams, reservoirs). However, Hantush's (1967) solution for a horizontal aquifer base is commonly used. To address sloping aquifers, a new closed-form analytical solution for water table mound accounts for the geometry and orientation of recharge sources at the land surface with respect to the aquifer base dip...

Deducing the state of a dynamical system as a function of time from a limited number of concurrent system state measurements is an important problem of great practical utility. A scheme that accomplishes this is called an "observer." We consider the case in which a model of the system is unavailable or insufficiently accurate, but "training" time series data of the desired state variables are available for a short period of time, and a limited number of other system variables are continually measured. We propose a solution to this problem using networks of neuron-like units known as "reservoir computers...

Development of highly concentrated formulations of protein and peptide drugs is a major challenge due to increased susceptibility to aggregation and precipitation. Numerous drug delivery systems including implantable and wearable controlled-release devices require thermally stable formulations with high concentrations due to limited device sizes and long-term use. Herein we report a highly concentrated insulin gel formulation (up to 80 mg/mL, corresponding to 2200 IU/mL), stabilized with a non-ionic amphiphilic triblock copolymer (i...