Article
Chemistry, Physical
Sezer Sorgun, Hakan Kucuk, Kahraman Birgin
Summary: Topological indices are numerical invariants associated with molecular structures and are helpful in characterizing many properties, especially in estimating biological activities. This paper formulates distance-based topological indices for certain polysaccharides, such as Chitosan, Chitin, and Cellulose.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Mathematics
Aiman Arshad, Aqsa Sattar, Muhammad Javaid, Mamo Abebe Ashebo
Summary: Graph theory is widely used in cheminformatics to develop physicochemical, chemical structure, and property models. By employing numerical structure invariants, chemical graph details can be manipulated and studied. This article focuses on the study of topological indices based on connection numbers, such as the Zagreb index and modified Zagreb index. The results of these indices are obtained through the analysis of Cartesian product and numerical calculations.
JOURNAL OF MATHEMATICS
(2023)
Article
Mathematics
Muhammad Basit Ali, Ebenezer Bonyah, Muhammad Javaid
Summary: In this paper, we obtained various topological indices for Sudoku graphs, including Zagreb connection indices and multiplicative Zagreb connection indices.
JOURNAL OF MATHEMATICS
(2022)
Article
Mathematics
Durbar Maji, Ganesh Ghorai, Muhammad Khalid Mahmood, Md. Ashraful Alam
Summary: The study focuses on the inverse problem based on topological indices, specifically on the Y-index, Gourava indices, second hyper-Zagreb index, reformulated first Zagreb index, and reformulated F-index.
JOURNAL OF MATHEMATICS
(2021)
Article
Chemistry, Organic
Zehui Shao, Akbar Jahanbani, Seyed Mahmoud Sheikholeslami
Summary: With the rapid development of the manufacture of medicines, a wide range of new drugs emerge each year. In this study, we analyzed the drug molecular structure and calculated several indices related to their medical properties. Surfaces associated with these indices were plotted using Maple 15 for comparison.
POLYCYCLIC AROMATIC COMPOUNDS
(2022)
Article
Chemistry, Organic
Neha Kansal, Pravin Garg, Omendra Singh
Summary: This article computes the temperature topological indices of several COVID-19 drugs and demonstrates their correlation with the physico-chemical properties. This theoretical approach can aid in predicting the qualities of COVID-19 drugs before experimentation, benefiting the pharmaceutical industry.
POLYCYCLIC AROMATIC COMPOUNDS
(2023)
Article
Mathematics
Saima Parveen, Nadeem Ul Hassan Awan, Mogtaba Mohammed, Fozia Bashir Farooq, Nisha Iqbal
Summary: This paper discusses the use of topological indices to study the physicochemical properties of drugs used to treat diabetes, and their correlation with these properties.
JOURNAL OF MATHEMATICS
(2022)
Article
Chemistry, Organic
Lei Huang, Yong Wang, K. Pattabiraman, P. Danesh, Muhammad Kamran Siddiqui, Murat Cancan
Summary: The threat of cancer therapy has been present for several decades, affecting nearly 10 million people worldwide each year. There are various types of anticancer medications, including hormones, antimetabolites, and alkalizing agents. This planned research examines the potential of antiviral medications for cancer treatment by analyzing their chemical structure and alkane characteristics. Additionally, topological indices based on status distance are computed using ST-polynomials, which are used to estimate the physicochemical properties of these medications through QSPR models.
POLYCYCLIC AROMATIC COMPOUNDS
(2023)
Article
Mathematics
Aftab Hussain, Muhammad Numan, Nafisa Naz, Saad Ihsan Butt, Adnan Aslam, Asfand Fahad
Summary: The paper explored two classes of Benes networks and derived closed-form expressions for some of their topological indices. Additionally, the fourth version of GA and the fifth version of ABC indices were calculated for these network classes.
JOURNAL OF MATHEMATICS
(2021)
Review
Chemistry, Medicinal
Karanpreet Singh Bhatia, Ankit Kumar Gupta, Anil Kumar Saxena
Summary: Quantitative Structure-Activity Relationship (QSAR) studies are important in drug discovery research, and they involve correlating biological activity with physicochemical and structural descriptors. Topological indices (TIs) play a crucial role in drug discovery, but have a lack of physicochemical interpretation which is essential for understanding the mechanism of action. This review discusses the advances in TIs, their physicochemical significance, and their role in developing QSAR models.
CURRENT TOPICS IN MEDICINAL CHEMISTRY
(2023)
Article
Computer Science, Information Systems
Yuede Ma, Matthias Dehmer, Urs-Martin Kuenzi, Shailesh Tripathi, Modjtaba Ghorbani, Jin Tao, Frank Emmert-Streib
Summary: This paper investigates the usefulness of topological graph measures and finds that many measures fail to solve problems effectively due to the selection of redundant and unfavorable graph invariants, as well as the lack of reflection in defining these measures. The paper extends the debate in the literature and quantitatively studies the usefulness of topological indices by assigning a feature vector to graphs that contains 'useful' properties represented by certain measures. The paper demonstrates examples and compares the usefulness using distance measures and an agglomerative clustering task.
INFORMATION SCIENCES
(2022)
Article
Chemistry, Physical
Jia-Bao Liu, Micheal Arockiaraj, M. Arulperumjothi, Savari Prabhu
Summary: The world is facing challenges in controlling the spread of COVID-19 due to the lack of proper drugs for treatment. Utilizing molecular topology has become an important approach for drug design, where structurally related molecules show similar pharmacological properties, aiding in the identification of new drugs. This study investigates the structural properties of various antiviral drugs and their topological indices, providing valuable insights for the development of new drugs for COVID-19.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2021)
Article
Mathematics, Applied
Sumiya Nasir, Nadeem ul Hassan Awan, Fozia Bashir Farooq, Saima Parveen
Summary: A topological index is a real number derived from the chemical graph structure and can predict the physicochemical and biological properties of anticancer drugs. This article discusses drugs used to treat blood cancer and reveals a strong correlation between topological indices and the physicochemical properties of these drugs.
Article
Chemistry, Multidisciplinary
Xiujun Zhang, Zainab Saeed Bajwa, Shahid Zaman, Sidra Munawar, Dan Li
Summary: This article discusses the application of topological indices in predicting the effectiveness of anti-cancer drugs, focusing on the mathematical relationships between these indices and physicochemical characteristics.
Article
Chemistry, Physical
Siman Li, Li Shi, Wei Gao
Summary: This study investigated the redefined Zagreb indices, forgotten index, reduced reciprocal Randic index, and reduced second Zagreb index for random polyphenyl chains and random spiro chains generated by zeroth-order Markov process, discussing their applications in the fields of materials and pharmacology.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2021)
Article
Mathematics, Applied
Jose M. Amigo, Roberto Dale, Piergiulio Tempesta
Summary: Permutation entropy is a method to measure the complexity of deterministic time series through data symbolic quantization, and is increasingly popular due to its convergence properties and computational efficiency. However, it may diverge in certain scenarios, but a generalized permutation entropy proposed in this paper addresses this issue and has been shown to be practical and effective in numerical simulations.
Review
Physics, Multidisciplinary
Adrian Hernandez, Jose M. Amigo
Summary: Deep learning models and GPUs have revolutionized machine learning, while attention mechanisms offer a promising solution for sequential reasoning, aiding in modeling complex systems effectively.
Article
Statistics & Probability
Jose M. Amigo, Angel Gimenez, Oscar Martinez-Bonastre, Jose Valero
Summary: The paper reviews stochastic models of data congestion control on the Internet, discusses the transformation from random to deterministic models, and sheds light on complex processes such as Internet data traffic. The results are expected to aid in designing active queue management algorithms under real conditions.
STOCHASTICS AND DYNAMICS
(2021)
Article
Chemistry, Multidisciplinary
Jose M. Amigo, Guillem Duran, Angel Gimenez, Jose Valero, Oscar Martinez Bonastre
Summary: This article focuses on modeling a new AQM scheme using Petri nets, incorporating a discrete dynamical model and new parameters for better stability control over router queue length oscillations. The study validates the model through matrix equation approach, reachability tree, and invariant analysis, confirming key properties such as reachability, boundedness, reversibility, deadlock, and liveness.
APPLIED SCIENCES-BASEL
(2021)
Article
Mathematics, Applied
Jose M. Amigo, Roberto Dale, Piergiulio Tempesta
Summary: This paper presents new results on permutation complexity and permutation entropy, and introduces a unified approach to ordinal analysis of deterministic and random processes through complexity classes.
COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION
(2022)
Article
Chemistry, Medicinal
Maria Galvez-Llompart, Riccardo Zanni, Ramon Garcia-Domenech, Jorge Galvez
Summary: Despite being considered an orphan disease, amyotrophic lateral sclerosis (ALS) is seeing a rapid increase in prevalence, making it difficult to find effective treatments. Computational methods based on receptors or ligands have the potential to improve the success rate of potential drug candidates and reduce resources and time. This study presents a computational strategy based on Molecular Topology to create a reliable tool for identifying and repurposing potential drugs for ALS treatment in the early stages.
Article
Biochemistry & Molecular Biology
Maria Galvez-Llompart, Riccardo Zanni, Jorge Galvez, Subhash C. Basak, Sagar M. Goyal
Summary: This study demonstrates the potential of drug repurposing in tackling pandemics. The researchers identified molecules with anti-SARS-CoV-2 activity through in silico screening and validated their effectiveness in vitro.
Review
Mathematics, Applied
Jose M. Amigo, Roberto Dale, Piergiulio Tempesta
Summary: This review discusses group entropy and its application to permutation complexity. A new approach to complexity in time series analysis based on permutation entropy and group entropy is revisited. The results show that the permutation entropy rate can be extended to random processes, providing a unified framework to discuss chaotic and random behaviors.
Article
Agriculture, Multidisciplinary
Riccardo Zanni, Jesus Martinez-Cruz, Maria Galvez-Llompart, Dolores Fernandez-Ortuno, Diego Romero, Ramon Garcia-Domenech, Alejandro Perez-Garcia, Jorge Galvez
Summary: Fungicide resistance is a serious issue in modern agriculture, and the development of new and environmentally friendly chemicals is in high demand. In this study, a computational strategy based on quantitative structure-activity relationship (QSAR) and molecular topology (MT) was used to discover potential chitin deacetylase (CDA) inhibitors. The identified inhibitors showed fungicidal activity and the ability to stimulate the plant immune system, making them promising candidates for combating resistant fungal species.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Editorial Material
Physics, Multidisciplinary
Jose M. Amigo, Piergiulio Tempesta
Article
Biochemistry & Molecular Biology
Angela Garcia-Garcia, Jesus Vicente de Julian-Ortiz, Jorge Galvez, David Font, Carles Ayats, Maria del Remedio Guna Serrano, Carlos Munoz-Collado, Rafael Borras, Jose Manuel Villalgordo
Summary: A method for identifying molecular scaffolds active against Mycobacterium tuberculosis complex (MTBC) has been developed. A mathematical model based on topological descriptors was constructed and validated, with an accuracy of over 86% in discriminating active and inactive compounds. The model was also effective in selecting potential antituberculosis compounds and several new compounds showed activity in vitro.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Angel Gimenez, Miguel A. Murcia, Jose M. Amigo, Oscar Martinez-Bonastre, Jose Valero
Summary: In this paper, a simple and robust RED-type algorithm, along with its dynamic variants, is presented to improve the performance of TCP/IP networks. These algorithms can adapt to different network environments and user needs, maintaining a stable queue length and adjusting dynamically according to changing network traffic conditions.
APPLIED SCIENCES-BASEL
(2022)
Review
Mathematics, Applied
Yoshito Hirata, Jose M. Amigo
Summary: Discretization of nonlinear time series can be achieved through partitioning, permutations, recurrence plots, and horizontal visibility graphs. This review summarizes and compares these methods from the perspective of symbolic dynamics, which offers a suitable framework for studying symbolic representation and reconstruction of nonlinear time series.
Article
Mathematics, Applied
Pawel Pilarczyk, Grzegorz Graff, Jose M. Amigo, Katarzyna Tessmer, Krzysztof Narkiewicz, Beata Graff
Summary: The paper introduces an entropy-based classification method for quantifying mutual dependencies in heart rate and beat-to-beat blood pressure recordings. Machine learning is used to select a subset of suitable indices to build an optimal model for distinguishing patients with obstructive sleep apnea from a control group.
Article
Clinical Neurology
Marcelo Galarza, Volkan Etus, Fidel Sosa, Romina Arganaraz, Beatriz Mantese, Roberto Gazzeri, Christian Garcia Montoya, Pedro de la Rosa, Antonio Lopez Guerrero, Gerald Chaban, Angel Gimenez, Jose Maria Amigo
Summary: The homogeneous flow pattern of the ventricular catheter represents a next generation design that shows promising results in reducing obstructions during the treatment of hydrocephalus.
CHILDS NERVOUS SYSTEM
(2021)
