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Provided herein are methods and composition for trackable genetic variant libraries. Further provided herein are methods and compositions for recursive engineering. Further provided herein are methods and compositions for multiplex engineering. Further provided herein are methods and compositions for enriching for editing and trackable engineered sequences and cells using nucleic acid-guided nucleases.
In this paper we consider a new generalized algorithm for the efficient calculation of component object volumes given their equivalent constructive solid geometry (CSG) definition. The new method relies on domain decomposition to recursively subdivide the original component into smaller pieces with volumes that can be computed analytically or stochastically, if needed. Unlike simpler brute-force approaches, the proposed decomposition scheme is guaranteed to be robust and accurate to within a user-defined tolerance. The new algorithm is also fully general and can handle any valid CSG component definition, without the need for additional input from the user. The new technique has been specifically optimized to calculate volumes of component definitions commonly found in models used for Monte Carlo particle transport simulations for criticality safety and reactor analysis applications. However, the algorithm can be easily extended to any application which uses CSG representations for component objects. The paper provides a complete description of the novel volume calculation algorithm, along with a discussion of the conjectured error bounds on volumes calculated within the method. In addition, numerical results comparing the new algorithm with a standard stochastic volume calculation algorithm are presented for a series of problems spanning a range of representative component sizes and complexities. (authors)
Quantitative analysis in software development has been a challenging topic over the years in safety software. While qualitative processes for vigorous safety software verification and validation (V and V) have been provided through standard such as IEEE 1012, quantitative analysis for V and V tasks such as correctness, completeness or accuracy evaluation have not been formally defined. In practice, there are quantitative analyses in terms of using software metrics. Many of these software metrics are useful in analyzing the test results. Some of them are used for providing guidance in code evaluation activities e.g. numbers of line of codes not exceeding certain limits, recursive calls are not allowed, etc. However, few can be used for providing quantitative analysis guidance for the V and V tasks such as completeness evaluation. AREVA Federal Services (AFS) has provided services for many nuclear projects in US. Through compliance with IEEE 1012, AFS V and V processes have provided vigorous qualitative processes ensuring quality level of the software products used in the project meeting the required nuclear software level. In addition, quantitative analysis is developed to provide structured validation framework ensuring 'zero defect' in the software products. This paper describes some aspects of the quantitative approaches using a sample safety application. (authors)
We consider the problem of controlling the frequency response of weakly-coupled multi-machine multi-inverter low-inertia power systems via grid-forming inverter-based resources (IBRs). In contrast to existing methods, our approach relies on dividing the larger system into multiple strongly-coupled subsystems, without ignoring either the underlying network or approximating the subsystem response as an aggregate harmonic mean model. Rather, through a structured clustering and recursive dynamic shaping approach, the frequency response of the overall system to load perturbations is shaped appropriately. We demonstrate the proposed approach for a three-node triangular configuration and a small-scale radial network. Furthermore, for small-scale radial microgrids, we demonstrate the ability of IBRs to tune the effective transfer functions of synchronous machines. This enables us to relax the uniform turbine time-constant assumptions and widen the scope of existing synchronization results for proportionally heterogeneous machines.
With the growing scarcity of freshwater, innovative process design mechanisms like Reverse Osmosis (RO) are increasingly gaining attention among water treatment utilities to address the rising demand. Ensuring reliable water production necessitates efficient resource utilization, minimizing downtime in (ultra-filtration) UF systems. Recent advancements in machine learning (ML) have enabled the development of accurate data-driven models for Model Predictive Control (MPC), often requiring minimal prior knowledge of underlying physical processes. In this study, we present predictive regression models based on Random Forest (RF) and Auto-Regressive (AR) approaches to forecast the initial Trans-Membrane Pressure (TMP) for each filtration cycle in data generated by Direct Potable Reuse (DPR) systems. The proposed RF-based model demonstrates superior performance compared to baseline methods, including historical mean, Last Observation Carried Forward (LOCF), and naïve AR models, across various forecasting horizons in terms of root mean square error (RMSE) metric. To evaluate how different classes of process variables contribute to TMP dynamics over time, we examine the feature importance of independent covariates across multiple forecast horizons. This analysis provides insight into the temporal relevance of operational and sensor-derived features, guiding control and monitoring strategies. Additionally, the impact of hyperparameter tuning on TMP prediction performance is studied for both direct and recursive RF modelling approaches across increasing forecast horizons. Accurate prediction of initial TMP is critical for optimizing RO operations, as it enables the development of robust modelling frameworks by accurately estimating membrane fouling trends, thereby enhancing process efficiency and long-term reliability. The demonstrated efficacy of the RF-based approach highlights its potential as a tool for real-time decision-making in water treatment systems, paving the way for advanced process optimization and sustainable water resource management.
Advanced reactors promise enhanced safety, greater efficiency, and waste reductions. To fully realize these benefits, it is crucial to address the need for autonomous or semi-autonomous control systems that require fewer operators. This research primarily supports the MARVEL autonomous control system, which requires real-time operation. However, the current RELAP5 reactor thermal hydraulic transient simulation is excessively time-consuming. Therefore, this study aims to leverage deep learning techniques to develop a surrogate model, providing a more efficient and accurate alternative for real-time performance. The model was trained using a combination of one-timestep prediction and scheduled sampling. It was then used for recursive prediction of the reactor state. This developed surrogate model significantly improves computational efficiency, achieving a 12 times acceleration.
We find a general formula for the two-loop renormalization counterterms of a scalar quantum field theory with interactions containing up to two derivatives, extending ’t Hooft’s one-loop result. The method can also be used for theories with higher derivative interactions, as long as the terms in the Lagrangian have at most one derivative acting on each field. We show that diagrams with factorizable topologies do not contribute to the renormalization group equations. The results in this paper will be combined with the geometric method in a subsequent paper to obtain the counterterms and renormalization group equations for the scalar sector of effective field theories (EFT) to two-loop order.
Vibration monitoring is a critical aspect of assessing the health and performance of machinery and industrial processes. This study explores the application of machine learning techniques, specifically the Random Forest (RF) classification model, to predict and classify chatter—a detrimental self-excited vibration phenomenon—during machining operations. While sophisticated methods have been employed to address chatter, this research investigates the efficacy of a novel approach to an RF model. The study leverages simulated vibration data, bypassing resource-intensive real-world data collection, to develop a versatile chatter detection model applicable across diverse machining configurations. The feature extraction process combines time-series features and Fast Fourier Transform (FFT) data features, streamlining the model while addressing challenges posed by feature selection. By focusing on the RF model’s simplicity and efficiency, this research advances chatter detection techniques, offering a practical tool with improved generalizability, computational efficiency, and ease of interpretation. The study demonstrates that innovation can reside in simplicity, opening avenues for wider applicability and accelerated progress in the machining industry.
Objective: To evaluate predictive factors of recurrent biliary obstruction (RBO) following percutaneous uncovered metal stent placement for unresectable distal malignant biliary obstruction (MBO) by using a competing risk model. Materials and Methods: Between March 2012 and March 2016, 119 patients underwent percutaneous uncovered metal stent placement with distal MBO at our institution. Univariate and multivariate analyses were conducted to identify the prognostic factors for RBO using a competing risk model. Results: The median overall survival period was 170 days (range 19–775 days). Recurrent biliary obstruction before death was observed in 34 patients (28.6%). The 3-, 6-, and 12-month cumulative incidences of RBO were 14.3%, 21.0%, and 27.7%, respectively. A multivariate analysis indicated that ampullary carcinoma compared with metastatic carcinoma (hazard ratio [HR] = 4.86; 95% confidence interval [CI], 1.74–13.54; P = 0.003) and a stent insertion above the sphincter of Oddi (HR 2.49; 95% CI, 1.11–5.62; P = 0.028) were the independent risk factors for RBO when we considered death to be a competing risk. Conclusion: Ampullary carcinoma and stent insertion above the sphincter of Oddi were risk factors for RBO in these patients who received percutaneous transhepatic stent placement.
We obtain sufficient conditions of solvability of the group pursuit problem for one or several evaders in recurrent differential games with equal opportunities of all players.
We consider a discrete dynamical system consisting of a number of controllable objects whose dynamics is governed by vector nonlinear discrete recurrent relations with control parameters and perturbations (noises). In such system, two levels of making management decisions are distinguished: the dominating (first) level and the subordinate (second) level, which have different criteria of functioning. These levels are integrated by certain information and control relations. We consider the problem of two-level minimax program terminal control in a discrete dynamical system and propose its mathematical statement and a general scheme of its solution.
By using the method of compliance functions and the Hankel transformation of the first order, we propose a procedure for the solution of the problem of torsion of a multilayer plate with elastic links between the layers. Two auxiliary functions connected with the transforms of stresses and displacements at the points of the top boundary of the layer are introduced for each layer. The recurrence relations for the auxiliary functions and the compliance functions of neighboring layers of the plate are constructed. For a two-layer plate, we analyze the influence of the coefficients of elastic links and the geometric and mechanical parameters of layers on the distribution of stresses at points of the common boundary of the layers.
The inverse factorial series expansion for the ratio of products of gamma functions whose arguments are linear functions of the variable is found. A recurrence relation for the coefficients in terms of the Nørlund–Bernoulli polynomials is provided, and the half-plane of convergence is determined. The results obtained naturally supplement a number of previous investigations of the gamma ratios, which began in the 1930-ies. The expansion obtained in this paper plays a crucial role in the study of the behavior of the delta-neutral Fox’s H-function in the neighborhood of its finite singular point. A particular case of the inverse factorial series expansion is used in deriving a possibly new identity for the Nørlund–Bernoulli polynomials.
We discuss a fundamental characteristic of orthogonal polynomials, like the existence of a Lie algebra behind them, which can be added to their other relevant aspects. At the basis of the complete framework for orthogonal polynomials we include thus–in addition to differential equations, recurrence relations, Hilbert spaces and square integrable functions–Lie algebra theory. We start here from the square integrable functions on the open connected subset of the real line whose bases are related to orthogonal polynomials. All these one-dimensional continuous spaces allow, besides the standard uncountable basis (|x〉), for an alternative countable basis (|n〉). The matrix elements that relate these two bases are essentially the orthogonal polynomials: Hermite polynomials for the line and Laguerre and Legendre polynomials for the half-line and the line interval, respectively. Differential recurrence relations of orthogonal polynomials allow us to realize that they determine an infinite-dimensional irreducible representation of a non-compact Lie algebra, whose second order Casimir C gives rise to the second order differential equation that defines the corresponding family of orthogonal polynomials. Thus, the Weyl–Heisenberg algebra h(1) with C=0 for Hermite polynomials and su(1,1) with C=−1/4 for Laguerre and Legendre polynomials are obtained. Starting from the orthogonal polynomials the Lie algebra is extended both to the whole space of the L{sup 2} functions and to the corresponding Universal Enveloping Algebra and transformation group. Generalized coherent states from each vector in the space L{sup 2} and, in particular, generalized coherent polynomials are thus obtained. -- Highlights: •Fundamental characteristic of orthogonal polynomials (OP): existence of a Lie algebra. •Differential recurrence relations of OP determine a unitary representation of a non-compact Lie group. •2nd order Casimir originates a 2nd order differential equation that defines the corresponding OP family. •Generalized coherent polynomials are obtained from OP.
We construct an expansion of the solutions of the bi-confluent Heun equation in terms of the Hermite functions. The series is governed by a three-term recurrence relation between successive coefficients of the expansion. We examine the restrictions that are imposed on the involved parameters in order that the series terminates thus resulting in closed-form finite-sum solutions of the bi-confluent Heun equation. A physical application of the closed-form solutions is discussed. We present the five six-parametric potentials for which the general solution of the one-dimensional Schrödinger equation is written in terms of the bi-confluent Heun functions and further identify a particular conditionally integrable potential for which the involved bi-confluent Heun function admits a four-term finite-sum expansion in terms of the Hermite functions. This is an infinite well defined on a half-axis. We present the explicit solution of the one-dimensional Schrödinger equation for this potential and discuss the bound states supported by the potential. We derive the exact equation for the energy spectrum and construct an accurate approximation for the bound-state energy levels. - Highlights: • The bi-confluent Heun functions are expanded in terms of the Hermite functions. • The restrictions leading to closed-form finite-sum solutions are identified. • The five bi-confluent Heun potentials for the Schrödinger equation are presented. • A new conditionally integrable Schrödinger potential is derived. • An accurate approximation for the bound-state energy levels is constructed.
We introduce an extended Kepler–Coulomb quantum model in spherical coordinates. The Schrödinger equation of this Hamiltonian is solved in these coordinates and it is shown that the wave functions of the system can be expressed in terms of Laguerre, Legendre and exceptional Jacobi polynomials (of hypergeometric type). We construct ladder and shift operators based on the corresponding wave functions and obtain their recurrence formulas. These recurrence relations are used to construct higher-order, algebraically independent integrals of motion to prove superintegrability of the Hamiltonian. The integrals form a higher rank polynomial algebra. By constructing the structure functions of the associated deformed oscillator algebras we derive the degeneracy of energy spectrum of the superintegrable system.
We investigate a complete normalized relativistic solutions for N-dimensional Hartmann potential and relativistic effects of non-central potential field for hydrogen molecule within the framework of asymptotic iteration approach. We also discuss in detail the influence of dimensions on the angular probability distribution of hydrogen molecule. N-dimensional bound state wavefunction solutions including angular and radial solutions are expressed in terms of the Jacobi and Laguerre polynomials, respectively. N-dimensional angular wavefunctions of hydrogen molecule were visualized with Matlab software. In hyperspherical coordinates, the recurrence relations between diagonal matrix elements have been derived for N-dimensional Hartmann potential in relativistic theory. We also obtain analytical expressions of diagonal matrix elements and the recurrence formula between off-diagonal matrix elements in N-dimensions.
In living cells, alpha-ketoacid decarboxylases (KDCs, EC 4.1.1.-) are a class of enzymes that convert alpha-ketoacids into aldehydes through decarboxylation. These aldehydes serve as either drop-in chemicals or precursors for the biosynthesis of alcohols, carboxylic acids, esters, and alkanes. These compounds play crucial roles in cellular metabolism and fitness and the bioeconomy, facilitating the sustainable and renewable biomanufacturing of platform chemicals and fuels. This review explores the diversity and classification of KDCs, detailing their structures, mechanisms, and functions. We highlight recent advancements in repurposing KDCs to enhance their efficiency and robustness for biomanufacturing. Additionally, we present modular KDC-dependent metabolic pathways for the microbial biosynthesis of aldehydes, alcohols, carboxylic acids, esters, and alkanes. Lastly, we discuss recent developments in the modular cell engineering technology that can potentially be applied to harness the diversity of KDC-dependent pathways for biomanufacturing platform chemicals and fuels.