Article
Biochemical Research Methods
Nousheen Parvaiz, Asma Abro, Syed Sikander Azam
Summary: Protein Tyrosine Phosphatase 1B (PTP1B) is a negative regulator of insulin signaling pathways and has potential as a medicinal target. This study explores the binding and conformational orientation of zinc(II) complexes in PTP1B using advanced computational methods. The findings suggest that zinc(II) complexes can bind to important residues in the enzyme and inhibit its activity.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Jerica Wilson, Bahrad A. Sokhansanj, Wei Chuen Chong, Rohan Chandraghatgi, Gail L. Rosen, Hai-Feng Ji
Summary: Fragment-based drug design is a computer-aided drug discovery method, however, it has limitations in processing time and success rate. In this study, a new method called Fragment Databases from Screened Ligands Drug Design (FDSL-DD) was proposed, which intelligently incorporates fragment characteristics into the drug design process to improve the binding affinity between drugs and protein targets.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
M. Chamani, G. H. Farrahi
Summary: This paper employs the Generalized Particle (GP) method to simulate nanoindentation and nanoscratching, showing that this method maintains consistent atomic properties across different scales and achieves results consistent with full atomic simulations.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Mathematical & Computational Biology
Honglan Zhu, Xuebing Zhang, Hao Zhang
Summary: In this paper, we investigate a delayed diffusive predator-prey model affected by toxic substances. The boundedness and persistence property of the model are studied first. Conditions for the existence of steady state bifurcation, Hopf bifurcation, and Turing bifurcation are obtained by analyzing the characteristic equation. Moreover, the Hopf bifurcation induced by the delay is also studied. Theoretical results are verified by numerical simulation, showing the significant impact of toxic substances on the system dynamics.
INTERNATIONAL JOURNAL OF BIOMATHEMATICS
(2024)
Article
Ecology
Jorge Pena, Aviad Heifetz, Georg Noldeke
Summary: Cooperation usually becomes harder to sustain as groups become larger, but in some cases, increasing group size can increase the probability of cooperation. The expected payoff and the probability of provision of the public good vary with the cost of cooperation.
THEORETICAL POPULATION BIOLOGY
(2024)
Article
Mathematical & Computational Biology
Yan Zhang, Yuanhua Qiao, Lijuan Duan
Summary: This paper investigates the memristive multidirectional associative memory neural networks (MAMNNs) with mixed time-varying delays in modeling the abrupt synaptic connections in human brain's associative memory. It proves the existence, boundedness, and asymptotical almost periodicity of the solution using Lyapunov function. It also examines the uniqueness and global exponential stability of the almost periodic solution using a new Lyapunov function. The research extends the study on the periodic and almost periodic solutions of bidirectional associative memory neural networks. Numerical examples and simulations are provided to demonstrate the validity of the main results.
INTERNATIONAL JOURNAL OF BIOMATHEMATICS
(2024)
Article
Biology
Beatrix Rahnsch, Leila Taghizadeh
Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Jason W. Olejarz, Martin A. Nowak
Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Haruto Tomizuka, Yuuya Tachiki
Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Rongsheng Huang, Qiaojun Situ, Jinzhi Lei
Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti
Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker
Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Andy Gardner
Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Armindo Salvador
Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Iain Hunter, Raz Leib
Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid
Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biochemical Research Methods
Rafael Lopes Almeida, Vinicius Gonsalves Maltarollo, Frederico Gualberto Ferreira Coelho
Summary: This research explores the application of Graph Neural Networks (GNNs) in drug development to overcome cost and time limitations. By comparing different datasets and GNN architectures, it provides benchmarking research to guide future investigations and enhance the effectiveness of GNNs in drug discovery and design. While oversampling technique shows potential on imbalanced datasets, further research is needed to optimize its usage and explore alternative solutions for class imbalance.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biology
Oleg Gaidai, Vladimir Yakimov, Yuhao Niu, Zirui Liu
Summary: This study presents a new methodology for assessing pandemic risks in a national health system. The suggested approach addresses the highdimensionality and complex cross-correlations between regional observations, enabling accurate epidemiological risk forecasts for multi-regional biological and health systems.
Article
Biology
Kaicheng Yu, Qiang Gao, Zexue Lin, Fei Wang, Peng Zhang, Yongdan Liu, Lihua Lu
Summary: Material extrusion has shown promise in tissue engineering, but the shape of 3D structures is currently uncontrollable. This study proposes a method to regulate the temperature gradient in the printing space by varying the height and internal diameter of the enclosure, which successfully avoids collapse and improves the height of scaffolds.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
