Article
Pharmacology & Pharmacy
Dominik Borrmann, Andreas Danzer, Gabriele Sadowski
Summary: Anomalous water-sorption kinetics in amorphous solid dispersions (ASDs) are caused by the slow swelling of the polymer. A diffusion-relaxation model using the Williams-Landel-Ferry (WLF) equation and the Arrhenius equation was used to predict the anomalous water-sorption kinetics in ASDs of poly(vinyl-pyrrolidone)-co-vinyl-acetate (PVPVA) and indomethacin (IND) at 25 degrees C. The model showed qualitative and quantitative agreement with experimental data, suggesting the potential for predicting diffusion-controlled release or swelling-controlled release behavior of ASDs.
Article
Materials Science, Multidisciplinary
C. McNamara, J. M. Rickman, H. M. Chan
Summary: The study investigates the microstructural evolution that initiates from a compositionally inhomogeneous patterned structure in solid-state reactions and uses reaction-diffusion formalism to model the process. By connecting the spatio-temporal evolution of the product phase with the geometry and chemistry of the starting duplex structure, a better understanding of reaction kinetics and product microstructures is obtained. The results can be used to select templates judiciously to promote the formation of desirable microstructures and quantify important experimental kinetic parameters.
Article
Cell Biology
Shin-ichiro Takebayashi, Tyrone Ryba, Kelsey Wimbish, Takuya Hayakawa, Morito Sakaue, Kenji Kuriya, Saori Takahashi, Shin Ogata, Ichiro Hiratani, Katsuzumi Okumura, Masaki Okano, Masato Ogata
Summary: Multiple epigenetic pathways, including DNA methylation, influence DNA replication timing. Loss of Dnmts has complex and diverse effects on the mammalian DNA replication landscape, with subtle but reproducible changes observed in various genomic regions. Replication timing in pericentromeric heterochromatin is correlated with redistribution of H3K27me3 induced by DNA hypomethylation.
Article
Biochemical Research Methods
Zeeshan Abbas, Mobeen Ur Rehman, Hilal Tayara, Kil To Chong
Summary: In this article, a unique artificial intelligence-based technique called ORI-Explorer is developed to recognize origins of replication sites (ORIs) in four different eukaryotic species. ORI-Explorer combines multiple feature engineering techniques and utilizes the CatBoost Classifier. It outperforms existing predictors and provides key insights into model success through the SHapley Additive exPlanation method. ORI-Explorer aims to aid community-wide efforts in discovering potential ORIs and developing verifiable biological hypotheses.
Review
Physics, Multidisciplinary
Thomas Andrew Waigh, Nickolay Korabel
Summary: A wide variety of phenomena in cellular and molecular biology involve anomalous transport, which is often heterogeneous in time and space. Single anomalous exponents and generalized diffusion coefficients fail to adequately describe these phenomena, requiring different experimental techniques and theoretical tools for analysis. High throughput analysis techniques and machine learning play important roles in the study of anomalous transport.
REPORTS ON PROGRESS IN PHYSICS
(2023)
Article
Physics, Multidisciplinary
Bao Wen, Ming-Gen Li, Jian Liu, Jing-Dong Bao
Summary: The ergodic hypothesis in statistical mechanics, which states that the long-time average is the same as the ensemble average, is closely related to irreversibility and increasing entropy. However, the time average of an observable quantity may be a random variable with a narrowing distribution width over time. This study focuses on the time-dependent fluctuation width of the time average for the velocity and kinetic energy of a force-free particle, considering the stationary velocity autocorrelation function.
Article
Multidisciplinary Sciences
Xinyu Gu, Nicholas P. Schafer, Peter G. Wolynes
Summary: This paper discusses the mechanism of translational control of messenger RNA through RNA-binding proteins, explores the role of prions in locally controlling translation in dendritic spines, and the factors influencing translation in different structured mRNA/protein aggregates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Physics, Multidisciplinary
Joachim H. Rosenberger, Tobias Goeppel, Patrick W. Kudella, Dieter Braun, Ulrich Gerland, Bernhard Altaner
Summary: Research has revealed the existence of two distinct length scales in the self-assembly of complex informational polymers from prebiotic building blocks, representing the onset of a strongly nonequilibrium regime and a local concentration maximum. This finding helps to understand the role of structure-forming processes in the early stages of prebiotic evolution.
Article
Chemistry, Multidisciplinary
Adrian Leathers, Michal Walczak, Ryan A. Brady, Assala Al Samad, Jurij Kotar, Michael J. Booth, Pietro Cicuta, Lorenzo Di Michele
Summary: This study introduces a platform for constructing membraneless artificial cells through the self-assembly of synthetic DNA nanostructures, enabling the formation of heterogeneous structures with localized functionalities. The method allows for up to five distinct concentric environments and functional segregation in artificial cells.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Engineering, Chemical
Yilin Yang, Siddarth K. Achar, John R. Kitchin
Summary: This study demonstrates the use of automatic differentiation (AD) in the evaluation of the degree of rate control (DRC). Compared to numerical derivatives, AD provides higher accuracy solutions with lower computational cost. The study also illustrates a hybrid local-global sensitivity analysis method that benefits from AD to efficiently assess the importance of kinetic parameters in an uncertain space.
Article
Multidisciplinary Sciences
Chun-Yi Cho, Charles A. Seller, Patrick H. O'Farrell
Summary: During the S phase in metazoans, the replication of different parts of the genome is coordinated in a temporal program. The mechanism controlling the timing and coordination of origin firing is not fully understood. In this study, researchers found that Rif1, an inhibitor of DNA replication, recruits PP1 and counteracts the firing of origins by S-phase kinases. They also discovered that the activity level of the S-phase kinase DDK affects the dispersal of Rif1 hubs, and that the recruited PP1 retards this dispersal. This study proposes a model in which the spatial and temporal coordination of late replication in the mid-blastula transition (MBT) embryo is controlled by self-stabilizing Rif1-PP1 hubs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Hui Zhang
Summary: DNA replication licensing is tightly regulated in eukaryotic cells to ensure proper replication initiation and prevent re-replication, with key mechanisms involving degradation of Cdt1 protein by CRL4(Cdt2) ubiquitin E3 ligase. The interaction between Cdt1 and PCNA, facilitated by the PIP box domain, plays a crucial role in this process, highlighting the importance of regulating DNA replication and genome stability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Antonino Scandurra, Valentina Iacono, Stefano Boscarino, Silvia Scalese, Maria Grazia Grimaldi, Francesco Ruffino
Summary: Non-enzymatic electrochemical glucose sensors play a crucial role in biomedical applications, enabling portable diabetic testing kits and continuous glucose monitoring systems. Nanostructured materials offer several advantages, such as high sensitivity and reduced dependence on analyte diffusion near the electrode-solution interface. This study focuses on modeling the chronoamperometric response of four electrodes made of nanostructured gold onto graphene paper.
Article
Chemistry, Physical
Won Seok Lee, Takafumi Enomoto, Aya Mizutani Akimoto, Ryo Yoshida
Summary: In this study, a fabrication method was established to analyze the volumetric self-oscillatory behaviors of submillimeter-sized spherical self-oscillating gels. It was found that the gels exhibited isotropic volumetric oscillations during the BZ reaction, and the oscillatory behaviors depended on the molar composition of NAPMAm in the gels and the concentration of Ru(bpy)(3)-NHS solution. These findings bridge knowledge gaps in the field and have potential applications in soft actuators.
Article
Physics, Multidisciplinary
S. Vitali, P. Paradisi, G. Pagnini
Summary: Through intensive simulations, it has been shown that the characteristic features of anomalous diffusion can be explained by a random walk driven by two different Markovian hopping-trap mechanisms. By studying ensemble and single-particle observables, it is found that this model matches the main characteristics of anomalous diffusion commonly observed in living systems. The transition of the walker's distribution from exponential to stretched-exponential and finally to Gaussian distribution can be observed by considering the inclusion of non-Gaussian intervals.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
