Article
Thermodynamics
Anna G. Knyazeva, Mariia A. Anisimova
Summary: This paper presents a model of the interaction between a solid particle and a metal melt within the framework of the theory of reactive diffusion in the coupled formulation. The diffusion and mechanical equilibrium problem are solved independently in a quasistationary formulation. The mechanical stresses and growth of a new phase are calculated and found to have time-dependent functions. The diffusion coefficient's explicit dependence on the stress work has been solved for the first time, allowing for the understanding of the mechanical properties' effect on the growth rate of the new phase. The generalized problem can be extended to the formation of multiple new phases.
INTERNATIONAL COMMUNICATIONS IN HEAT AND MASS TRANSFER
(2023)
Article
Biology
Jong Il Ahn, Liang Zhang, Harsha Ravishankar, Lixin Fan, Klara Kirsch, Yan Zeng, Lingjun Meng, Jung-Eun Park, Hye-Yeoung Yun, Rodolfo Ghirlando, Buyong Ma, David Ball, Bonsu Ku, Ruth Nussinov, Jeremy D. Schmit, William F. Heinz, Seung Jun Kim, Tatiana Karpova, Yun-Xing Wang, Kyung S. Lee
Summary: Structural, biophysical, and imaging data demonstrate that self-assembly of the pericentrosomal proteins Cep63 and Cep152 is a stepwise and concentration-dependent process. Defects in this process disrupt proper centriole duplication mediated by Plk4. This study provides insights into the organization and function of pericentriolar materials (PCM) and offers a potential model for studying PCM-related diseases in other species.
COMMUNICATIONS BIOLOGY
(2023)
Article
Engineering, Multidisciplinary
Raimund Burger, Julio Careaga, Stefan Diehl, Romel Pineda
Summary: Reactive settling refers to the process of solid particles settling in a fluid while simultaneously undergoing reactions with the liquid phase. It plays a crucial role in sequencing batch reactors in wastewater treatment plants. A mathematical model is used to describe the operational cycles of the reactor and a finite difference scheme is employed to simulate the denitrification process.
APPLIED MATHEMATICAL MODELLING
(2022)
Article
Multidisciplinary Sciences
Greg Davis, Allen J. York, Willis Clark Bacon, Suh-Chin Lin, Monica Malone McNeal, Alexander E. Yarawsky, Joseph J. Maciag, Jeanette L. C. Miller, Kathryn C. S. Locker, Michelle Bailey, Rebecca Stone, Michael Hall, Judith Gonzalez, Alyssa Sproles, E. Steve Woodle, Kristen Safier, Kristine A. Justus, Paul Spearman, Russell E. Ware, Jose A. Cancelas, Michael B. Jordan, Andrew B. Herr, David A. Hildeman, Jeffery D. Molkentin
Summary: This study investigated the SARS-CoV-2 infection rates in Greater Cincinnati area from August to December 2020. Different rates of infection were observed among different age groups, genders, and ethnicities. Geographic analysis revealed higher infection rates on the West side of Cincinnati and the lowest rates in the adjoining region of Kentucky.
Article
Mathematics, Interdisciplinary Applications
Muhammad Shahid, Kamran Usman
Summary: The behavior of single and paired solid particles in particulate flow, with varying shapes, orientations, and interactions, has been analyzed using numerical experiments. The study helps determine particle trajectories and interactions in a fluid channel.
COMPUTATIONAL PARTICLE MECHANICS
(2023)
Article
Engineering, Multidisciplinary
Raimund Burger, Julio Careaga, Stefan Diehl, Romel Pineda
Summary: This article proposes a numerical scheme for simulating reactive settling in sequencing batch reactors (SBRs) in wastewater treatment plants. The scheme utilizes a complex mathematical model to accurately describe the reactive settling process and has been validated through simulations.
APPLIED MATHEMATICAL MODELLING
(2022)
Article
Chemistry, Physical
Nathan P. Alexander, Ronald J. Phillips, Stephanie R. Dungan
Summary: Model equations for the Rayleigh ratio and the electric field autocorrelation function are derived using thermodynamic fluctuation theory applied to crowded solute-containing micellar solutions and microemulsions with negligible molecular species and polydispersity. The research investigates the influence of self-assembly on light scattering correlation functions and finds that self-assembly driven variations in micelle properties do not affect the scattering functions in the limit of zero local polydispersity.
Article
Chemistry, Physical
Nathan P. Alexander, Ronald J. Phillips, Stephanie R. Dungan
Summary: The study measured ternary diffusion coefficient matrices using the Taylor dispersion method for crowded aqueous solutions, finding that a theoretical model can accurately predict the results without adjustable parameters. The model, based on Batchelor's theory, showed good agreement with experimental data for concentrated mixtures.
Article
Environmental Sciences
Yukun Fan, Huan Jiang, Junli Ren, Xingxing Liu, Jianghu Lan, Peng Cheng, Qi Liu, Liangcheng Tan, Cheng Xue, Youbin Sun, Xiaolin Hou
Summary: Radionuclides are widely used for dating recent sediments, but their applicability can be limited by differences in sources, half-lives, environmental behavior, and measurement techniques. However, 239,240Pu shows significant advantages in sediment dating. Our study suggests that 239,240Pu can be a reliable tracer for rapidly accumulated sediment, and the input from surrounding soil erosion is an important source of sediment.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Mechanics
M. Pourjafar-Chelikdani, B. Taghilou, T. Rezaee, N. P. Khabazi, S. M. Taghavi, K. Sadeghy
Summary: In this study, the numerical investigation was conducted to study the effect of sinusoidal vibration on the settling dynamics of a circular particle in a viscoplastic fluid obeying the regularized Bingham-Papanastasiou model. The solid particle was modeled as a highly viscous Newtonian droplet, and the finite element method was used to solve the motion equations for the particle and the surrounding fluid. The numerical results closely matched the theoretical critical Bingham number for settling circular particles in Bingham materials. It was found that stuck particles can be excited to fall in the viscoplastic fluid if the amplitude of vibration exceeds a minimum value for a given frequency. The size and density of the particle were predicted to affect the threshold amplitude, and vibration was found to have an accelerating effect on particle settling, although the effect was non-monotonic.
Article
Mathematics
Shangjiang Guo
Summary: In this paper, a Lotka-Volterra competition-diffusion system with a focus on the nonlinear balance between interior reaction and boundary flux is studied. The global dynamics, including the existence, stability, and bifurcation of steady-state solutions, are analyzed based on competition coefficients, growth rate functions, and boundary reaction functions. The results significantly extend the existing literature on Lotka-Volterra competition-diffusion systems, including those with homogeneous boundary conditions.
JOURNAL OF DIFFERENTIAL EQUATIONS
(2023)
Article
Multidisciplinary Sciences
Michelle Cutajar, Fabrizio Andriulo, Megan R. Thomsett, Jonathan C. Moore, Benoit Couturaud, Steven M. Howdle, Robert A. Stockman, Stephen E. Harding
Summary: A novel polyhydroxylated monomer was synthesized from sustainable terpene feedstock derived from pine trees and used to prepare a polymer for wood consolidation purposes. Extensive characterization revealed the polymer's elongated shape, hydrogen bonding potential, and suitable molecular weight for further consideration as a potential consolidant.
SCIENTIFIC REPORTS
(2021)
Article
Mathematics, Applied
Shangzhi Li, Shangjiang Guo
Summary: In this paper, the existence, stability, local and global bifurcation of steady-state solutions for a diffusive logistic model with nonlinear boundary conditions are investigated. The supercritical and subcritical bifurcation of steady-state solutions are obtained using the Crandall-Rabinowitz theorem and the Lyapunov-Schmidt reduction. The local stability and the possibility of obtaining an Allee effect are also analyzed. Furthermore, the result on global bifurcation is obtained by employing the Rabinowitz theorem.
APPLIED MATHEMATICS LETTERS
(2023)
Article
Mathematics, Applied
Sudeshna Ghosh, Rekha Panghal
Summary: We investigated the settling of a flexible circular particle in two dimensions submerged in a Newtonian, viscous, and incompressible fluid due to gravity. The immersed boundary method (IBM) was used to solve the fluid-structure interaction. A parametric study was conducted to analyze the effect of different values of structure density and fluid viscosity on the settling velocity and distortion of the flexible particle. The results showed that the terminal velocity of the flexible particle increased with higher flexibility of the structure. It was also observed that a decrease in fluid viscosity led to more significant distortion in the particle, and heavier particles experienced greater distortion compared to lighter ones.
COMPUTATIONAL & APPLIED MATHEMATICS
(2022)
Article
Polymer Science
Brittany K. Roopnarine, Spencer C. Schmidt, Kevin J. Maxwell, Svetlana Morozova
Summary: Understanding the transport and thermodynamics of polymers in confined spaces is beneficial for separation processes. By studying the diffusion coefficient of dextran and sodium polyacrylate in convex lens-induced confinement, we can gain insights into how these polymers interact and improve separation processes.
Article
Biochemistry & Molecular Biology
Alexander E. Yarawsky, Stefanie L. Johns, Peter Schuck, Andrew B. Herr
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Chemistry, Physical
Luiza L. Knittel, Huaying Zhao, Ai Nguyen, Antonio Miranda, Peter Schuck, Alioscka A. Sousa
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Multidisciplinary Sciences
Alexander E. Conicella, Rui Huang, Zev A. Ripstein, Ai Nguyen, Eric Wang, Thomas Lohr, Peter Schuck, Michele Vendruscolo, John L. Rubinstein, Lewis E. Kay
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Microbiology
Zhaochun Chen, Ronald E. Engle, Chen-Hsiang Shen, Huaying Zhao, Peter W. Schuck, Emily J. Danoff, Hanh Nguyen, Norihisa Nishimura, Kevin W. Bock, Ian N. Moore, Peter D. Kwong, Robert H. Purcell, Sugantha Govindarajan, Patrizia Farci
Article
Biophysics
Huaying Zhao, Ai Nguyen, Samuel C. To, Peter Schuck
Summary: Analytical ultracentrifugation (AUC) provides absolute measurements of macromolecular parameters, but many instruments suffer from significant systematic errors. External calibration can greatly improve measurement precision and consistency.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Article
Biochemical Research Methods
Susan M. Clardy, David H. Lee, Peter Schuck
Summary: Advances in polymer science have expanded the applications of protein-polymer conjugates as biopharmaceuticals and biotechnology reagents. This study demonstrates the use of multisignal sedimentation velocity analytical ultracentrifugation to measure the polymer-to-protein ratio in antibody-drug conjugates of varying ratios and heterogeneity levels. The results show that multisignal sedimentation velocity can accurately provide crucial information on attributes like polymer-to-protein ratio.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Robert W. Harkness, Yuki Toyama, Zev A. Ripstein, Huaying Zhao, Alexander I. M. Sever, Qing Luan, Jacob P. Brady, Patricia L. Clark, Peter Schuck, Lewis E. Kay
Summary: DegP is an oligomeric protein with dual protease and chaperone activity that regulates protein homeostasis and virulence factor trafficking in gram-negative bacteria. Different oligomeric states are adopted by DegP to facilitate its function, with resting hexamers formed when not engaged to substrates and cage or bowl-like structures formed when bound to substrates, leading to increased proteolytic activity. The self-assembly mechanism of apo-DegP involves an ensemble of oligomeric states mediated by self-assembly of trimers, which can shift towards larger oligomeric assemblies under physiological conditions to respond to biological insults.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Erik W. Martin, Tyler S. Harmon, Jesse B. Hopkins, Srinivas Chakravarthy, J. Jeremias Incicco, Peter Schuck, Andrea Soranno, Tanja Mittag
Summary: This study investigates the assembly kinetics of a prion-like domain using liquid-liquid phase separation and identifies two kinetic regimes on different timescales characterized by the size distribution of clusters. The research uncovers the nucleation mechanisms of biological protein phase separation and reveals multiple kinetic regimes on the micro- to millisecond timescale.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Antonio Rodriguez-Blazquez, Arturo Carabias, Alba Moran-Vaquero, Sergio de Cima, Juan R. Luque-Ortega, Carlos Alfonso, Peter Schuck, Jose Antonio Manso, Sandra Macedo-Ribeiro, Carmen Guerrero, Jose M. de Pereda
Summary: C3G activation is regulated by phosphorylation and interaction with Crk adaptor proteins, revealing a two-factor mechanism for tight control of its activity.
CELL COMMUNICATION AND SIGNALING
(2023)
Article
Multidisciplinary Sciences
Huaying Zhao, Di Wu, Sergio A. Hassan, Ai Nguyen, Jiji Chen, Grzegorz Piszczek, Peter Schuck
Summary: The N-protein of SARS-CoV-2 plays a crucial role in viral assembly and RNA scaffolding. It promotes LLPS, forming dense droplets that aid in the assembly of ribonucleoprotein particles. Through experiments, simulations, and mutational analysis, researchers have discovered an unknown oligomerization site that contributes to LLPS and is necessary for the assembly of protein-nucleic acid complexes. This finding presents a potential target for antiviral therapeutics.
Article
Microbiology
Peter Schuck, Huaying Zhao
Summary: Molecular mimicry of short linear interaction motifs is a key mechanism for viral proteins to bind host domains and hijack host cell processes. Through analyzing the sequence diversity of SARS-CoV-2, this study reveals that motif mimicry is a highly dynamic process that can broadly explore host motifs, allowing the virus to rapidly evolve the virus-host interface.
Article
Multidisciplinary Sciences
Huaying Zhao, Ai Nguyen, Di Wu, Yan Li, Sergio A. Hassan, Jiji Chen, Hari Shroff, Grzegorz Piszczek, Peter Schuck
Summary: Global SARS-CoV-2 sequencing efforts have identified mutations in the spike protein and other viral proteins, with the mutational landscape of the nucleocapsid protein exhibiting more variability than the spike protein. The N-G215C mutation in the Delta variant may stabilize protein-protein interaction interfaces and enhance viral assembly efficiency, leading to greater infectivity. Through biophysical experiments, it was found that the N-G215C mutation shifts the unliganded protein from a dimeric to a tetrameric state, suggesting high plasticity in the N-protein's biophysical properties.
Review
Chemistry, Multidisciplinary
Alioscka A. Sousa, Peter Schuck, Sergio A. Hassan
Summary: The use of nanoparticles in biomedicine has transitioned from concept to clinical trials, with ultrasmall nanoparticles showing potential applications in diagnosis and therapy. The ability to control the behavior of these nanoparticles is limited, and further advances are needed in nanoengineering and chemical synthesis to fully understand their interactions in biological environments.
NANOSCALE ADVANCES
(2021)
Article
Medicine, Research & Experimental
Sumit K. Chaturvedi, Arun Parupudi, Kristian Juul-Madsen, Ai Nguyen, Thomas Vorup-Jensen, Sonia Dragulin-Otto, Huaying Zhao, Reza Esfandiary, Peter Schuck
Article
Chemistry, Multidisciplinary
Andre L. Lira, Rodrigo S. Ferreira, Ricardo J. S. Torquato, Maria Luiza Oliva, Peter Schuck, Alioscka A. Sousa
NANOSCALE ADVANCES
(2019)