Quasi-integrability and nonlinear resonances in cold atoms under modulation.

Quantum dynamics of a collection of atoms subjected to phase modulation has been carefully revisited. We present an exact analysis of the evolution of a two-level system (represented by a spinor) under the action of a time-dependent matrix Hamiltonian. The dynamics is shown to evolve on two coupled potential energy surfaces (PESs): one of them is binding, while the other one is scattering type. The dynamics is shown to be quasi-integrable with nonlinear resonances. The bounded dynamics with intermittent scattering at random moments presents a scenario reminiscent of Anderson and dynamical localization. We believe that a careful analytical investigation of a multi-component system that is classically non-integrable is relevant to many other fields, including quantum computation with multi-qubit systems.

CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration.

The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search, and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.

Applications of surface-enhanced Raman spectroscopy in environmental detection.

As the human population grows, the anthropogenic impacts from various agricultural and industrial processes produce unwanted contaminants in the environment. The accurate, sensitive and rapid detection of such contaminants is vital for human health and safety. Surface-enhanced Raman spectroscopy (SERS) is a valuable analytical tool with wide applications in environmental contaminant monitoring. The aim of this review is to summarize recent advancements within SERS research as it applies to environmental detection, with a focus on research published or accessible from January 2021 through December 2021 including early-access publications. Our goal is to provide a wide breadth of information that can be used to provide background knowledge of the field, as well as inform and encourage further development of SERS techniques in protecting environmental quality and safety. Specifically, we highlight the characteristics of effective SERS nanosubstrates, and explore methods for the SERS detection of inorganic, organic, and biological contaminants including heavy metals, pharmaceuticals, plastic particles, synthetic dyes, pesticides, viruses, bacteria and mycotoxins. We also discuss the current limitations of SERS technologies in environmental detection and propose several avenues for future investigation. We encourage researchers to fill in the identified gaps so that SERS can be implemented in a real-world environment more effectively and efficiently, ultimately providing reliable and timely data to help and make science-based strategies and policies to protect environmental safety and public health.

Graphene nanoflakes on transparent glass electrode sensor for electrochemical sensing of anti-diabetic drug.

Metformin (Mf) plays a major role in controlling insulin level of individuals at risk of developing diabetes mellitus. Overdose of Mf can cause lactic acidosis, diarrhoea, cough, or hoarseness, etc. These particulars point out the identification for selective and sensitive methods of Mf determination. In the present work, graphene nanoflakes-polymethylene blue (GNF-PMB) nano-composites were developed onto fluorine-doped tin oxide (SnO2/F) coated glass substrates for electrochemical sensing of Mf using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The developed sensor shows quick response time (10 s), linearity as 10-103 µM, LOD (0.1 nM), and good shelf life (10 weeks). Attempts have been made to utilize this electrode for estimation of Mf in urine samples. Configured as a highly responsive, reproducible Mf sensor, it combines the electrical properties of GNF and stable electron transfer of PMB. The newly developed Mf sensor presents a promising candidate in point-of-care diagnosis.