Article
Multidisciplinary Sciences
Jan Kessler, Francesco Calcavecchia, Thomas D. Kuehne
Summary: Inspired by the universal approximation theorem and the widespread adoption of artificial neural network techniques, feed-forward neural networks are proposed as a general purpose trial wave function for quantum Monte Carlo simulations of continuous many-body systems. The accuracy of the trial wave functions was demonstrated by studying an exactly solvable model system of two trapped interacting particles and the hydrogen dimer. The whole many-body wave function can be represented by a neural network for simple model systems, while the antisymmetry condition of non-trivial fermionic systems is incorporated by means of a Slater determinant.
ADVANCED THEORY AND SIMULATIONS
(2021)
Article
Chemistry, Physical
Robert F. Bull, Alfred C. K. Farris, David P. Landau
Summary: In this study, we investigated the thermodynamic and structural properties of synthetic multiblock copolymers using Wang-Landau sampling on a simple cubic lattice. We compared different sequences and observed differences in the collapse process, as well as studied structural transitions below the coil-to-globule transition temperature in the lattice. Additionally, we examined the relationship between block length, number of blocks, and overall polymer length with respect to these structural transitions, and observed how the formation and shape of a ground state core affected structural changes as temperature increased.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Computer Science, Information Systems
Yair Daon, Amit Huppert, Uri Obolski
Summary: DOPE, a novel pooling strategy based on the Bayesian D-optimal experimental design criterion, defines optimal pooled tests by maximizing the mutual information between data and infection states. Compared to other common pooling strategies and individual testing, DOPE shows lower error rates while utilizing fewer tests, and maintains this dominance across various infection prevalence values. It provides posterior infection probability distributions, incorporates prior information, and can be easily extended with new COVID-19 information.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2021)
Article
Biochemistry & Molecular Biology
Joao N. C. Especial, Antonio Rey, Patricia F. N. Faisca
Summary: Monte Carlo simulations are a powerful technique used in various fields for sampling equilibrium ensembles and calculating thermodynamic and structural properties. The preservation of linear topology is crucial for obtaining correct equilibrium results, especially for complex structures.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Materials Science, Multidisciplinary
Owen Bradley, George G. Batrouni, Richard T. Scalettar
Summary: The Holstein Hamiltonian describes fermions interacting with phonons on a lattice. It predicts the behavior of dressed quasiparticles and the formation of superconducting and charge density wave phases at different densities. Quantum Monte Carlo calculations have been used to determine critical temperatures for these phase transitions in various lattice geometries.
Article
Materials Science, Multidisciplinary
S. Tarat, Bo Xiao, R. Mondaini, R. T. Scalettar
Summary: This paper investigates the two mechanisms for the vanishing of the sign problem in quantum simulations: whether randomly chosen field configurations have negative det[M(h)], or if the specific subset of configurations chosen by the weighting function have a greater preponderance of negative values. By conducting auxiliary field quantum Monte Carlo simulations of interacting fermions, the relative importance of these two mechanisms can be better understood.
Article
Polymer Science
Jiang Zhang, Wenbing Hu
Summary: The effects of specific chain-end hydrogen-bonding interactions on the once-folding crystallization of 16-mers in PEG were investigated. It was found that these interactions have little influence on the kinetics of nucleation and lateral growth, but create a significant gap at the growth front, leading to the double-lamella phenomenon. The chain-end hydrogen-bonding interactions are abundant at the surfaces of once-folded lamellar crystals, enhancing their metastability and hindering their thickening into chain-extended crystals. Additionally, intra- and inter-molecular secondary nucleation at the folded and extended growth fronts exhibit different growth rate dependencies on the interaction strengths. The study reveals the role of specific chain-end interactions in PEG crystallization.
Article
Chemistry, Physical
Dilimulati Aierken, Michael Bachmann
Summary: We systematically investigate the effect of bending stiffness on the ground-state conformations of semiflexible polymers. The formation of different conformations depends strongly on the strength of the bending restraint, as observed through detailed analysis of contact and distance maps.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
R. Mondaini, S. Tarat, R. T. Scalettar
Summary: The sign problem is a fundamental limitation in simulations of strongly correlated matter. In this study, the quantitive connection between the sign problem in determinant quantum Monte Carlo (QMC) and quantum critical behavior is demonstrated through simulations of several well-understood models. A reinterpretation of the low average sign in the Hubbard model is proposed, relating it to the onset of pseudogap behavior and exotic superconductivity.
Article
Astronomy & Astrophysics
William Detmold, Gurtej Kanwar, Henry Lamm, Michael L. Wagman, Neill C. Warrington
Summary: Path integral contour deformations have been proposed as a solution to sign and signal-to-noise problems in lattice field theories, particularly those related to phase fluctuations. By defining a family of contour deformations suitable for SU(N) lattice gauge theory, these problems associated with complex actions and observables can be significantly reduced. Experimental results show that this approach can achieve a significant reduction in variance.
Article
Chemistry, Multidisciplinary
Langping Tu, Kefan Wu, Yongshi Luo, Enhui Wang, Jun Yuan, Jing Zuo, Ding Zhou, Bin Li, Jiajia Zhou, Dayong Jin, Hong Zhang
Summary: Relatively low efficiency is the bottleneck for the application of lanthanide-doped upconversion nanoparticles. The high-level doping strategy realized in recent years has not improved the efficiency as much as expected. This study combines theoretical simulation and spectroscopy to elucidate the role of cross relaxation (CR) in the upconversion process and demonstrates that inhibiting CR significantly improves upconversion efficiency.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Mechanics
M. Beljin-Cavic, I Loncarevic, Lj Budinski-Petkovic, Z. M. Jaksic, S. B. Vrhovac
Summary: This study uses Monte Carlo simulations to investigate the random sequential adsorption of mixtures of objects with varying shapes on a three-dimensional cubic lattice. The research focuses on the influence of geometrical properties of the shapes on the jamming coverage and temporal evolution of density. The results show that the coverage approaches the jamming limit exponentially and the relaxation time is determined by the number of orientations the objects can take on the lattice. The jamming coverage of a mixture can be greater than or in between the jamming coverages of the single-component shapes, depending on the local geometry.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Physics, Multidisciplinary
Aaram J. Kim, Katharina Lenk, Jiajun Li, Philipp Werner, Martin Eckstein
Summary: We propose a diagrammatic Monte Carlo approach for quantum impurity models, which is a generalization of the strong-coupling expansion for fermionic impurity models. The algorithm is based on a self-consistently computed three-point vertex and a stochastically sampled four-point vertex and provides numerically exact results in a wide parameter regime. The performance of the algorithm is demonstrated with applications to a spin-boson model representing an emitter in a waveguide. The spatial distribution of the photon density around the emitter is also discussed.
PHYSICAL REVIEW LETTERS
(2023)
Article
Mechanics
V Dossetti, G. M. Viswanathan, V. M. Kenkre
Summary: This article presents numerical investigations on the validity of the Boltzmann prescription in statistical mechanics for large systems. The study focuses on whether the extensivity of energy implies the extensivity of the Boltzmann entropy. Based on simulations considering a large number of states, the results suggest that the systems studied are still too small to conclusively settle the issues raised. However, the new approach outlined in this study represents a first step towards addressing the question of non-extensive statistical mechanics from first principles.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Physics, Fluids & Plasmas
Menahem Krief, Yinon Ashkenazy
Summary: The method for calculating elastic constants using MD simulation and EAM potential was studied, showing robust and accurate evaluation in NVT MD simulations. This method is applicable for various situations and provides fast and accurate results compared to traditional methods.
Article
Biochemical Research Methods
Monisha Elumalai, Andrey Ipatov, Joana Carvalho, Joana Guerreiro, Marta Prado
Summary: A new DNA target amplification strategy combined with dual-mode colorimetric naked eye and smartphone analysis is proposed for the rapid and sensitive detection of zebra mussel environmental DNA. This method demonstrates high specificity and sensitivity, suitable for field analysis of environmental samples without the need for expensive laboratory equipment.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Food Science & Technology
Foteini Roumani, Cristina Rodrigues, Jorge Barros-Velazquez, Alejandro Garrido-Maestu, Marta Prado
Summary: A rapid and reliable RPA-LF assay was developed for the detection of spoilage fungi in fruit-based products. The method showed high sensitivity and specificity, making it suitable for point of care applications.
FOOD ANALYTICAL METHODS
(2023)
Article
Chemistry, Analytical
Agnes Purwidyantri, Andrey Ipatov, Telma Domingues, Jerome Borme, Marco Martins, Pedro Alpuim, Marta Prado
Summary: This study developed a lab-on-a-chip by integrating a graphene field-effect transistor chip with a programmable microfluidic device for DNA detection. The graphene FET chip's real-time biochemical events were monitored through a portable graphene curve reader, and a fully automated programmable microfluidic system controlled the fluidic flow into the sensing interface. The system showed high sensitivity and reliability with a nine-graphene sensor layout on a single chip. The portable graphene curve reader provided tunable electrical parameter setup and easy data acquisition. Fluidic control was achieved through a multi-position valve, and the flow cell design and microfluidic system packaging offered high precision and portability. The merged system allowed for probe DNA immobilization, a blocking step, and DNA hybridization with stable signal output, even in long-run experimental setups. The proposed DNA sensor demonstrated high sensitivity and an outstanding limit of detection, making it one of the most sensitive sensors reported to date. The programmable device showcased essential versatilities in biomolecular detection in a fully portable and automated platform.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Food Science & Technology
Foteini Roumani, Jorge Barros-Velazquez, Alejandro Garrido-Maestu, Marta Prado
Summary: The application of rapid molecular-based methods and isothermal techniques has shown promise in detecting patulin-producing fungi, although it still faces limitations in distinguishing between live and dead microorganisms. By implementing specific DNA extraction protocols and detection methods, the developed assays were able to detect low concentrations of fungi effectively.
Article
Biochemistry & Molecular Biology
Cristina Pastrana, J. Rafaela L. Guerreiro, Monisha Elumalai, Carlos Carpena-Torres, Almudena Crooke, Gonzalo Carracedo, Marta Prado, Fernando Huete-Toral
Summary: Acanthamoeba keratitis is a rapidly progressing ocular pathology mainly caused by contact lens use. Early and differential diagnosis is crucial for preventing progression and improving prognosis. Current diagnosis techniques are time-consuming and expensive, highlighting the need for fast, accessible, and accurate detection methods. Researchers have developed a dual-mode colorimetric method using gold nanoparticles for rapid and accurate detection of Acanthamoeba, which can be detected by the naked eye or a smartphone.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Agnes Purwidyantri, Sarah Azinheiro, Aitor Garcia Roldan, Tereza Jaegerova, Adriana Vilaca, Rofer Machado, M. Fatima Cerqueria, Jerome Borme, Telma Domingues, Marco Martins, Pedro Alpuim, Marta Prado
Summary: Identifying grape varieties in wine and related products using DNA analysis is challenging due to their complexity and low DNA content. This study presents an integrated portable biosensor based on a monolayer graphene field-effect transistor array, which can distinguish closely related grapevine varieties and detect single-nucleotide polymorphisms. The biosensor operates at ultralow DNA concentrations with a high specificity and attomolar detection limit. It offers a promising way for decentralized analytical tools to track wine authenticity and contribute to the digitalization of the agro-food industry.
Correction
Food Science & Technology
Foteini Roumani, Cristina Rodrigues, Jorge Barros-Velazquez, Alejandro Garrido-Maestu, Marta Prado
FOOD ANALYTICAL METHODS
(2023)
Article
Chemistry, Analytical
Ana Costa-Ribeiro, Sarah Azinheiro, Soraia P. S. Fernandes, Alexandre Lamas, Marta Prado, Laura M. Salonen, Alejandro Garrido-Maestu
Summary: A low-cost sample treatment protocol was developed to remove inhibitory compounds from vegetables, enabling the rapid detection of STEC in ready-to-eat food samples within one day. The method showed high diagnostic sensitivity and specificity.
ANALYTICA CHIMICA ACTA
(2023)
Article
Chemistry, Applied
Amin Sajid, Christoph von Holst
Summary: In this study, DART-HRMS was used to accurately characterize feed additive formulations containing coccidiostats or carotenoids. The efficacy of DART-HRMS in identifying active substances and distinguishing between additives with the same active substance was demonstrated. The method involves extracting samples with organic solvents and measuring the extracts with DART-HRMS. Statistical tools, including factorial design and multivariate statistics, were employed to optimize the DART-HRMS settings and establish classification models for feed additive formulations. The study highlights the potential of DART-HRMS as a tool for compliance checks with EU regulations.
FOOD ADDITIVES AND CONTAMINANTS PART A-CHEMISTRY ANALYSIS CONTROL EXPOSURE & RISK ASSESSMENT
(2023)
Article
Chemistry, Applied
Veronica Maria Teresa Lattanzio, Biancamaria Ciasca, Emanuela Verdini, Christoph von Holst, Ivan Pecorelli
Summary: The design, execution and evaluation of an interlaboratory validation study for a LC-MS/MS method used in detecting polar pesticides in animal-derived food are reported. The study involved five participant laboratories who were asked to analyze test samples contaminated with 11 polar pesticides. The method showed high average recoveries and good repeatability and reproducibility, providing insights for its implementation by new users.
FOOD ADDITIVES AND CONTAMINANTS PART A-CHEMISTRY ANALYSIS CONTROL EXPOSURE & RISK ASSESSMENT
(2023)
Article
Food Science & Technology
Sarah Azinheiro, Pedro Rodriguez-Lopez, Antonio Lozano-Leon, Hugo Guedes, Patricia Regal, Carlos M. Franco, Alberto Cepeda, Pilar Teixeira, Luis D. R. Melo, Daniela Silva, Ana Fernandez, Marcia Faria, Foteini Roumani, Juan Herrera, Marta Prado, Marta Lopez-Cabo, Alejandro Garrido-Maestu
Summary: Listeria monocytogenes is a significant foodborne pathogen that infects vulnerable individuals through contaminated foods. A new qPCR-based method for detecting L. monocytogenes was evaluated in a study involving six laboratories in Spain and Portugal. The results showed high sensitivity and agreement with the reference method, indicating its potential for controlling the spread of L. monocytogenes.
Article
Biotechnology & Applied Microbiology
Alexandre Lamas, Silvio B. Santos, Marta Prado, Alejandro Garrido-Maestu
Summary: A same-day detection method combining Phage Amplification and Loop-mediated isothermal amplification (PA-LAMP) was developed to specifically detect viable S. Enteritidis in chicken breast. This method, based on the detection of phage DNA, showed improved sensitivity and capability to detect viable bacteria.
Article
Chemistry, Analytical
Alexandre Lamas, Sarah Azinheiro, Foteini Roumani, Marta Prado, Alejandro Garrido-Maestu
Summary: Loop-mediated isothermal amplification (LAMP) is the most popular isothermal nucleic acid amplification technique, which uses at least four primers, including outer (F3/B3) and inner primers (FIP/BIP). Inner primers hybridize in two distinct regions, and the usage of a linker, typically composed of four thymines, in the middle of these primers can improve assay performance. Additionally, dual-priming oligonucleotides (DPO) have been reported to provide highly specific amplification and reduce non-specific amplifications. The current study explored the suitability of replacing standard outer primers with DPO primers and their combination with different linker sequences in the inner primers. The results showed that replacing standard F3/B3 with DPO primers did not significantly affect the overall performance of the assay and provided additional stability to temperature changes, regardless of the type of linker implemented in the inner primers, with a linker composed of thymines performing the best.
Article
Polymer Science
Sara Pereira, Ana Costa-Ribeiro, Pilar Teixeira, Laura Rodriguez-Lorenzo, Marta Prado, Miguel A. Cerqueira, Alejandro Garrido-Maestu
Summary: Chitosan, derived from chitin, possesses antimicrobial activity. Its application as micro- or nanoparticles expands its usage. However, the size of chitosan nanoparticles produced from different starting materials affects their antimicrobial properties.
Article
Chemistry, Multidisciplinary
Carla Teixeira, Andrey Ipatov, Joana Carvalho, Agnes Purwidyantri, Natacha Fontes, Marta Prado
Summary: In recent years, efforts have been made to improve the DNA-based analysis by simplifying, miniaturizing, and reducing the time and cost of analysis. One important aspect is DNA extraction and purification, a crucial step for ensuring good analytical performance. In this work, a miniaturized module for DNA purification based on microscale solid phase extraction (mu SPE) using a borosilicate glass microfiber filter was developed. A highly efficient DNA purification protocol was also established for extracting DNA from vegetable samples of different varieties.
Article
Food Science & Technology
Ewelina Bigoraj, Iwona Kozyra, Agnieszka Kaupke, Zbigniew Osinski, James Lowther, Artur Rzezutka
Summary: The aim of this study was to assess the prevalence of human enteric viruses in mussels sold on the Polish market and study the fecal contamination of shellfish. The study found that human enteric viruses were commonly present in shellfish, with norovirus being the most frequently detected. The study also observed a seasonal distribution pattern of viruses in shellfish samples.
Editorial Material
Food Science & Technology
Bojan Blagojevic, Lis Alban Denmark
Article
Food Science & Technology
Indy Magnus, Fatemeh Abbasi, Hugo Thienpont, Lien Smeesters
Summary: Food safety and quality are increasingly important in our society, driving the development of novel optical food sensing technologies. However, current optical sensing technologies are often limited in their sensitivity and product variability. In this study, we developed a novel pistachio nut screening methodology using fluorescence spectroscopy and advanced chemometrics to simultaneously detect shells, tree parts, and aflatoxins. By optimizing hardware and software parameters, we achieved a high classification accuracy for healthy pistachio kernels.
Article
Food Science & Technology
Xiaodong Wang, Jingqiang Yu, Haixia Wu, Leiying Wu, Wuyunga Borjihan, Cong Wang, Munkhjargal Burenjargal, Alideertu Dong
Summary: This study developed a novel photon-phonon coupling (PPC) cold sterilization technology and compared its effects with low-temperature pasteurization and microwave ultraviolet. The results showed that PPC effectively reduced bacterial count in raw milk with minimal impact on milk quality and nutritional composition.
Review
Food Science & Technology
Riyadh Abdulmalek Hassan, Sharina Abu Hanifah, Lee Yook Heng, Fawaz Al-badaii, Alizar Ulianas
Summary: This study used bibliometric visualisation map analysis to explore the publication outputs, trends, and hotspots for endocrine disruptors (EDMs) biosensor development in relation to mycotoxins. The analysis showed that the current literature primarily focuses on developing biosensors for detecting highly toxic and widely distributed mycotoxins in food, but there needs to be more focus on biosensors for detecting mycotoxins known as endocrine disruptors.
Article
Food Science & Technology
Yajie Zheng, Jianpeng Dou, Changpo Sun, Hujun Liu, Shipei Zhang, Wenfu Wu
Summary: This study investigated the efficiency of modified SA/ll-glucan/Mt microsphere adsorbents in removing DON and ZEN from CSL. The microspheres showed high adsorption capacity, and simple and rapid regeneration was achieved without affecting the removal efficiency of mycotoxins from CSL.
Article
Food Science & Technology
Carlos Adelantado, Jose Angel Salatti-Dorado, Carlos Herrera, Lourdes Arce, Maria Jose Cardador
Summary: High-performance-ion mobility spectrometry (HPIMS) was used for the first time in the analysis of olive oil samples, following a simple liquid-liquid extraction procedure. The developed methodology is user-friendly, fast, and inexpensive, complying with the principles of green chemistry. The proposed approach, combined with multivariate analysis, showed potential in classifying olive oil samples based on their organoleptic quality, with high accuracy rates.
Article
Food Science & Technology
Jia-Wen Wei, Jia-Rong He, Shi-Yi Chen, Yi-Han Guo, Xuan-Zhu Huo, Nuan Zheng, Shuo-Hui Cao, Yao-Qun Li
Summary: Polycyclic aromatic hydrocarbons (PAHs) are a major cause of human cancer. This study developed a quantitative analysis method for PAH4 using the back propagation neural network (BPNN) algorithm and constant wavelength synchronous fluorescence (CWSF) spectra as the data sets. The method can predict the concentrations of PAH4 in edible oil samples without preprocessing or pre-separation. It has been proven to be a powerful tool for the rapid detection of PAH4.
Article
Food Science & Technology
Liyun Chen, Xiumei Li, Jingyi Chen, Ranxun Lin, Yuhan Mai, Yuxin Lin, Guodong Wang, Zheng Chen, Wei Zhang, Jiang Wang, Cai Yuan, Longguang Jiang, Peng Xu, Mingdong Huang
Summary: Food spoilage is primarily caused by microbial contamination. Curcumin has shown moderate antimicrobial activity as a food preservative. This study formulates curcumin with zinc acetate to enhance its efficacy, resulting in Cur-Zn with increased antimicrobial activity against multiple food-contaminating bacteria and fungi. With light illumination, the antimicrobial activity of Cur-Zn is further enhanced due to the photodynamic inactivation (PDI) effect.
Article
Food Science & Technology
Marta Pilar Ortiz-Moriano, Gonzalo Machado-Schiaffino, Eva Garcia-Vazquez, Alba Ardura
Summary: Mislabelling in the global fisheries sector raises concerns about the identity, safety, and sustainability of seafood products. This study examined mislabelling in shrimps and prawns sold in the Spanish market and assessed potential risks of heavy metal ingestion.
Article
Food Science & Technology
Doyeon Kim, Jinwoo Kim, Minsik Kim
Summary: This study demonstrates the enhanced bactericidal activity of engineered lysins fused with amphipathic antimicrobial peptides against Gram-negative bacterium Cronobacter sakazakii. The fusion lysins are capable of disrupting bacterial cells and significantly reducing the risk of infection within a certain range of temperature and pH. Additionally, the study also shows the bactericidal effect of these fusion lysins against other Gram-negative pathogens.
Article
Food Science & Technology
Seul-Ki Park, Kyung-Jin Cho, Du-Min Jo, Young-Mog Kim
Summary: This study presents a new approach for detecting pathogenic Vibrio spp. in contaminated seafood, which combines PCR with a simplified DNA extraction process and pre-culturing step. The method has been validated and shown to be efficient, time-saving, and highly sensitive, offering a potential alternative for improving safety measures in the food industry.
Article
Food Science & Technology
Suwimol Surareungchai, Chaleeda Borompichaichartkul, Chitsiri Rachtanapun, Nutthachai Pongprasert, Pongphen Jitareerat, Varit Srilaong
Summary: This study builds upon previous research and focuses on risk assessment and analysis in the organic salad industry. The results show that previous risk matrix models can be adapted for various raw materials, and preventive control plans can be applied across different aspects of the production process.
Article
Food Science & Technology
Xuan Zhang, Changling Fang, Xiaoyi Lou, Feng Han, Siman Li, Yongfu Shi, Dongmei Huang
Summary: This study aimed to assess the levels of Biogenic amines (BAs) in four common food types in the Chinese market. It was found that cheese and seafood derived product showed higher levels of BAs, and the histamine level in mackerel and yellow rice wine exceeded the limits.
Article
Food Science & Technology
Martina Foschi, Alessandra Biancolillo, Federico Marini, Francesco Cosentino, Francesca Di Donato, Angelo Antonio D'Archivio
Summary: This study aimed to develop a potentially non-destructive and routine-compatible method for the geographical traceability of high-valued Italian chickpeas. By analyzing the spectral information of the outer and inner parts of the kernels, it was found that the spectral analysis of the outer part yielded accurate and reliable results, indicating the possibility of non-destructive authentication.
