Article
Chemistry, Physical
Fumio Oosawa
Summary: The history of the birth of the Asakura-Oosawa theory is presented in the article.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Mathematical & Computational Biology
Tingting Ding, Tongqian Zhang
Summary: This paper investigates a stochastic SIRS epidemic model with information intervention, and examines the asymptotic behavior of the solutions by constructing an appropriate Lyapunov function. The results show that the average in time of the second moment of the solutions is bounded for a relatively small noise. Additionally, the study finds that the information interaction response rate plays an active role in disease control.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2022)
Article
Physics, Fluids & Plasmas
F. Leyvraz
Summary: The paper presents the scaling theory of irreversible aggregation, showing that cluster size distribution rapidly decays to zero for sizes much larger or much smaller than the typical size. An unexpected subleading correction is discovered for clusters much larger than the typical size, and results beyond the scaling limit are obtained, revealing deviations from the expected behavior.
Article
Mathematics, Applied
Fengling Liu, Nangao Zhang, Changjiang Zhu
Summary: This paper investigates the asymptotic behavior of solutions to the Cauchy problem and initial-boundary value problem of the one-dimensional Keller-Segel model. For the Cauchy problem, the solutions are shown to time-asymptotically converge to a nonlinear diffusion wave. For the initial-boundary value problem, the asymptotic profile remains a self-similar solution in the case of Dirichlet boundary condition, and the global existence and asymptotic behavior of solutions near constant steady states are established in the case of null-Neumann boundary condition.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2023)
Article
Mathematics, Applied
Yuming Qin, Xiaolei Dong, Xin Liu
Summary: This paper investigates the global existence and asymptotic behavior of solutions in Hi(i=1,2,4) in the one-dimensional infrarelativistic model of a compressible viscous gas with radiation, under suitable hypotheses on the transport coefficients. It improves upon previous results in Qin et al. (2014).
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2023)
Article
Mathematics, Applied
A. A. Rey, A. C. Frery, J. Gambini, M. M. Lucini
Summary: Ordinal patterns are a powerful technique for revealing latent dynamics in time series data. This study focuses on the computation of the asymptotic distribution of permutation entropy, considering the correlation structure of the inherent patterns. Simulation algorithms for sampling time series with prescribed histograms of patterns and transition probabilities between them are presented to better understand the intricacies of ordinal patterns and their statistical attributes.
Article
Mathematics, Interdisciplinary Applications
Xinguang Zhang, Peng Chen, Hui Tian, Yonghong Wu
Summary: In this article, the iterative properties of positive solutions for a tempered fractional equation are investigated. By weakening a basic growth condition, new and complete results on the iterative properties of the positive solutions to the equation are established, including the uniqueness and existence of positive solutions, the convergence of the iterative sequence to the unique solution, the error estimate and convergence rate of the solution, as well as the asymptotic behavior of the solution.
FRACTAL AND FRACTIONAL
(2023)
Article
Engineering, Mechanical
Hua Wu
Summary: A partial-limit method has been developed to understand solutions related to real eigenvalues for the Fokas-Lenells equation. By applying this method, new multiple-pole solutions with different eigenvalues and properties can be obtained. The procedure may be extended to other integrable systems, offering the potential to generate new solutions.
NONLINEAR DYNAMICS
(2021)
Article
Mechanics
Xuyao Yuan, Wei Wei, Zhenlong Fang, Yong Chen
Summary: In this work, a simple, stable, and purely local pressure-based double-population lattice Boltzmann model is proposed for low-Mach number variable-density flow. The model recovers the continuity, momentum, and energy equations describing the flow and accurately predicts the drag coefficient and Nusselt number for different Reynolds numbers.
Article
Mathematics, Applied
Satoru Iwasaki
Summary: In this study, we analyze the asymptotic behavior of global solutions to forest kinetic model equations consisting of young trees, old trees, and air-borne seeds. We prove the asymptotic convergence of global solutions to a stationary solution under certain parameter assumptions by demonstrating a non-smooth version of the Lojasiewicz-Simon gradient inequality and a norm estimate of the time derivative of global solutions on a suitable functional space.
NONLINEAR ANALYSIS-REAL WORLD APPLICATIONS
(2021)
Article
Mathematics
Ikki Fukuda, Masahiro Ikeda
Summary: In this study, we investigate the large time behavior of solutions to the Cauchy problem for the BBM-Burgers equation. We show that the solution approaches the self-similar solution to the Burgers equation, known as the nonlinear diffusion wave. Additionally, we construct the appropriate second asymptotic profiles of the solutions based on the initial data. Through this discussion, we analyze the effect of the initial data on the long time behavior of the solution and derive the optimal asymptotic rate to the nonlinear diffusion wave. Moreover, we obtain the second asymptotic profiles of the solutions with slowly decaying data, which has not been studied previously.
JOURNAL OF DIFFERENTIAL EQUATIONS
(2022)
Article
Water Resources
Ioannis Tsoukalas
Summary: The focus of this study is to estimate the distribution of maxima using non-asymptotic approaches, as classic extreme value theory and asymptotic properties may not be suitable for hydrological processes. The study revisits the problem from a non-asymptotic perspective and introduces a fast alternative model. Through simulations and comparisons, the study demonstrates that non-asymptotic approaches can model the distribution of maxima with reduced uncertainty and variability, particularly for intermittent processes like rainfall. The study also discusses the theoretical estimation of the multi-scale probability of obtaining a zero value and provides step-by-step recipes and an R package.
HYDROLOGICAL SCIENCES JOURNAL
(2022)
Article
Engineering, Mechanical
Dimiter Prodanov
Summary: This study provides a parametric solution and two exponential analytical asymptotic solutions for the SIR model in epidemic outbreaks, which can be used for estimation of the COVID-19 pandemic in six European countries.
NONLINEAR DYNAMICS
(2023)
Article
Transportation Science & Technology
Jorge A. Laval
Summary: This paper presents additional results of the generalized bathtub model for urban networks, including a simpler derivation and exact solutions for uniformly distributed trip lengths. It is shown that the trip-based model is equivalent to the accumulation-based model in steady state, and that the trip-length distribution has only a transient effect on traffic dynamics. A queueing approximation method is proposed to compute the network accumulation variance and it is found that the accumulation variance is larger than predicted by traditional queueing models, indicating the nonlinear dynamics imposed by the macroscopic fundamental diagram. The system exhibits critical behavior near the capacity state where the accumulation variance diverges, suggesting the potential usefulness of tools from critical phenomena and phase transitions for understanding congestion in cities.
TRANSPORTATION RESEARCH PART C-EMERGING TECHNOLOGIES
(2023)
Article
Mathematics, Applied
Yuqiu Wu, Jingxue Yin, Liangwei Wang, Zhengwen Tu
Summary: This paper considers the relationships between the solutions of a fourth-order parabolic equation and the solutions for this equation with absorption, and finds that the solutions of this equation with absorption can exhibit complicated asymptotic behaviors.
APPLIED MATHEMATICS LETTERS
(2021)
Article
Materials Science, Multidisciplinary
Yufan Xu, Hongjia Zhu, Yi Shen, Alexander P. M. Guttenplan, Kadi L. Saar, Yuqian Lu, Daniele Vigolo, Laura S. Itzhaki, Tuomas P. J. Knowles
Summary: Micron-scale soft materials have diverse applications in bioengineering and molecular medicine, as well as consumer products. Researchers have developed a microfluidic platform for measuring the shear modulus of individual microscale particles in a parallel manner. The results obtained using this platform are consistent with traditional serial measurements. This platform allows for in situ parallel measurements of the mechanical properties of soft micron-scale particles, and can be easily adapted for various applications using scalable single-layer soft-photolithography fabrication.
Review
Chemistry, Multidisciplinary
Yufan Xu, Hongjia Zhu, Akhila Denduluri, Yangteng Ou, Nadia A. Erkamp, Runzhang Qi, Yi Shen, Tuomas P. J. Knowles
Summary: This review discusses the applications and potential of microgels in various fields, including biomedical research, materials science, and bioengineering. The synthesis of microgels using microfluidic technologies is a key enabling technology for tailoring their properties. Microgels play important roles in liquid-liquid phase separation, micromechanics, biosensors, and regenerative medicine.
Article
Chemistry, Physical
Quentin A. E. Peter, Raphael P. B. Jacquat, Therese W. Herling, Pavan Kumar Challa, Tadas Kartanas, Tuomas P. J. Knowles
Summary: Living systems are highly spatially inhomogeneous, which can fundamentally change the behavior of biomolecular species, including proteins. In this study, an improved diffusiophoresis microfluidic technique was used to measure protein diffusiophoresis in real space. Individual proteins were found to undergo strong diffusiophoretic motion in salt gradients, leading to significant changes in their spatial organization. This phenomenon can also be used to control protein motion in microfluidic devices.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Daoyuan Qian, Thomas C. T. Michaels, Tuomas P. J. Knowles
Summary: In this study, a self-consistent analytical solution for the binodal concentrations of the two component Flory-Huggins phase separation model is derived. The derived form extends the validity range of Ginzburg-Landau expansion to cover the entire phase space. The analytical solution reveals an exponential scaling law of the dilute phase binodal concentration as a function of the interaction strength and chain length. This approach demonstrates its power by fitting experimental protein liquid-liquid phase separation boundaries and resolving differences in interaction energy contributions of individual amino acids.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Nanoscience & Nanotechnology
Zenon Toprakcioglu, Elizabeth G. Wiita, Akhila K. Jayaram, Rebecca C. Gregory, Tuomas P. J. Knowles
Summary: The emergence of drug-resistant bacteria and fungi is a global concern in healthcare. Developing effective small molecule therapeutic strategies is challenging, thus, exploring biomaterials with physical modes of action is an alternative approach. In this study, silk-based films embedded with selenium nanoparticles were found to exhibit antibacterial and antifungal properties while remaining biocompatible and noncytotoxic towards mammalian cells.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Qi Zhang, Zenon Toprakcioglu, Akhila K. Jayaram, Guangsheng Guo, Xiayan Wang, Tuomas P. J. Knowles
Summary: Nanoparticles have become increasingly important in biological applications, but obtaining stable and controlled protein nanoparticles has been challenging. In this study, we used droplet microfluidics to produce highly monodisperse protein nanoparticles by utilizing the characteristic of rapid and continuous mixing in microdroplets. The internal vortex flows within microdroplets were found to determine the uniformity of the nanoparticles, and by adjusting parameters such as protein concentration and flow rates, we were able to control the nanoparticle size. These protein nanoparticles showed high biocompatibility with HEK-293 cells and were able to fully enter the cells. Due to the high throughput and level of control, this approach has the potential for future intracellular drug delivery or gene transfection.
Article
Biochemistry & Molecular Biology
Ayaka Kamada, Zenon Toprakcioglu, Tuomas P. J. Knowles
Summary: The study uses the framework of chemical kinetics to reveal the molecular mechanisms of the self-assembly of regenerated silk fibroin. The results show that the aggregation of regenerated silk fibroin is dominated by a nonclassical secondary nucleation process, which is also influenced by shear flow. These findings contribute to a better understanding of the kinetics of protein fiber self-assembly.
Article
Biophysics
Matthias M. Schneider, Tom Scheidt, Ashley J. Priddey, Catherine K. Xu, Mengsha Hu, Georg Meisl, Sean R. A. Devenish, Christopher M. Dobson, Vasilis Kosmoliaptsis, Tuomas P. J. Knowles
Summary: Antibody profiling is essential in understanding humoral response in various diseases. By using microfluidic diffusional sizing (MDS), we successfully quantified the binding affinity and concentration of alloantibodies to HLA proteins, a widely used clinical biomarker in organ transplantation, in both buffer and crude human serum. Our assay offers a potential path for in-depth profiling of humoral immunity and further insights into the clinical relevance of antibody reactivity.
BIOSENSORS & BIOELECTRONICS
(2023)
Review
Chemistry, Multidisciplinary
Kadi L. Saar, Daoyuan Qian, Lydia L. Good, Alexey S. Morgunov, Rosana Collepardo-Guevara, Robert B. Best, Tuomas P. J. Knowles
Summary: Biomolecular condensation processes are fundamental mechanisms that living cells utilize to organize biomolecules in time and space, leading to the formation of membraneless organelles. Computational methods, including theoretical methods, physics-driven simulations, and data-driven machine learning methods, provide a unique perspective to study biomolecular condensation and offer advantages such as high resolution and scale. This review discusses the recent progress and limitations of these computational approaches and highlights the challenges in understanding the molecular driving forces and biological roles of biomolecular condensation in health and disease.
Article
Multidisciplinary Sciences
Nadia A. Erkamp, Tomas Sneideris, Hannes Ausserwoger, Daoyuan Qian, Seema Qamar, Jonathon Nixon-Abell, Peter St George-Hyslop, Jeremy D. Schmit, David A. Weitz, Tuomas P. J. Knowles
Summary: In this study, the authors investigate how biomolecular condensates can form an internal structure with dilute phase droplets via kinetic driving forces. The formation of biomolecular condensates through phase separation from proteins and nucleic acids is widely used by cells as a spatial organizational principle. This study demonstrates that complex internal architecture of condensates can arise from kinetic driving forces, providing insights into understanding and controlling the structure of condensates in vitro and in vivo.
NATURE COMMUNICATIONS
(2023)
Review
Physics, Applied
Thomas C. T. Michaels, Daoyuan Qian, Andela Saric, Michele Vendruscolo, Sara Linse, Tuomas P. J. Knowles
Summary: This Review discusses the general protein self-assembly behavior of amyloid fibrils, which is associated with functional biology and the development of diseases such as Alzheimer and Parkinson diseases. It summarizes recent progress in describing the biophysical features of amyloid self-assembly as a nucleation-and-growth process, highlighting the role of secondary nucleation. The Review also outlines non-classical aspects of aggregate formation and discusses their implications for understanding and modulating protein assembly pathways.
NATURE REVIEWS PHYSICS
(2023)
Article
Nanoscience & Nanotechnology
Kevin N. Baumann, Tim Schroeder, Prashanth S. Ciryam, Diana Morzy, Philip Tinnefeld, Tuomas P. J. Knowles, Silvia Hernandez-Ainsa
Summary: This study presents a method to achieve triggered drug release by forming a DNA mesh on large unilamellar liposomes. The programmability and adaptability of DNA nanoarchitectures in combination with liposomes prove to have great potential in drug delivery. The results demonstrate that the triggered-release mechanism can enhance the cytotoxicity of the loaded drug, suggesting its promising application in targeted drug delivery.
ACS APPLIED BIO MATERIALS
(2022)
Article
Nanoscience & Nanotechnology
Kevin N. Baumann, Tim Schroeder, Prashanth S. Ciryam, Diana Morzy, Philip Tinnefeld, Tuomas P. J. Knowles, Silvia Hernandez-Ainsa
Summary: In this study, a method was presented to form biocompatible hybrid carriers by combining DNA nanoarchitectures with liposomes, which can meet the requirements for drug release. The release of dye from the carriers was increased after triggering.
ACS APPLIED BIO MATERIALS
(2022)
Meeting Abstract
Biophysics
Naunehal S. Matharu, Chyi W. Chung, Janet R. Kumita, Gabriele S. Kaminski, Tuomas P. Knowles
BIOPHYSICAL JOURNAL
(2022)