Article
Polymer Science
Vincenzo Calabrese, Stylianos Varchanis, Simon J. Haward, Amy Q. . Shen
Summary: Understanding the hydrodynamic alignment of colloidal rods in polymer solutions is crucial for producing structurally ordered materials. This study analyzes the alignment of colloidal rods suspended in polymer solutions and compares it to the case where additional colloidal rods provide crowding in a pure solvent. The dynamics of the polymer is found to govern the shear-induced alignment of colloidal rods, with the Weissenberg number as the control parameter for alignment. Additionally, it is shown that the alignment of colloidal rods follows a universal trend regardless of the crowding environment.
Article
Biochemistry & Molecular Biology
Silvia De Sio, Jana Waegele, Twinkle Bhatia, Bruno Voigt, Hauke Lilie, Maria Ott
Summary: Amyloid (A..) is the main component of senile plaques in Alzheimer's disease, and it forms elongated fibrils through structural conversions. This study investigates the impact of macromolecular crowding on the fibrillation pathways of A.. 40 and A.. 42, the two most common peptide isoforms. The results show that while excluded volume effects imposed by crowding generally increase interaction rates and structural conversions, the specific effects vary depending on the peptide, crowder, and ionic strength. The study also reveals the entropic gain induced by the crowder.
MACROMOLECULAR BIOSCIENCE
(2023)
Article
Chemistry, Physical
Gaurav Chauhan, Michael L. Simpson, Steven M. Abel
Summary: Macromolecular crowding in cellular and cell-free systems can affect the interactions of semiflexible biopolymers with surfaces. The adsorption of semiflexible polymers on repulsive surfaces is promoted by stiffer polymers, smaller crowding particles, and larger volume fractions of crowders. Crowding-induced transitions from non-adsorbed to partially and strongly adsorbed states occur at smaller values of bending stiffness as the volume fraction of crowders increases.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biophysics
Wylie Stroberg, Santiago Schnell
Summary: In this study, an algorithm was developed to simulate reversible reactions between reacting Brownian particles, investigating the effect of macromolecular crowding on reaction rates and correlation times for ligand-receptor systems. It was found that crowding could increase the accuracy of estimated ligand concentration based on receptor occupancy, particularly by enhancing the effective association rates between small ligands and receptors. Crowding also decreased the accuracy of receptor's estimate for larger ligands by decreasing the microscopic association and dissociation rates.
BIOPHYSICAL JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Nidhi Chauhan, Kirti Saxena, Utkarsh Jain
Summary: Single molecule detection is crucial for understanding the physical and chemical properties as well as mechanisms involved in the normal functioning of body cells. This review highlights various traditional methods and biosensing technologies that offer single molecule sensitivity. The discussion includes plasmonic resonance, nanopores, whispering gallery mode, Simoa assay, recognition tunneling, as well as biosensor-based detection using plasmonic, SERS, CRISPR/Cas, and other types of biosensors. The review provides an overview of the progression in different techniques employed for single molecule detection.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Multidisciplinary Sciences
Birgit Koehn, Patricia Schwarz, Pernilla Wittung-Stafshede, Michael Kovermann
Summary: This study investigated the impact of molecular crowding on the binding capacity of DNA to protein, revealing that structural features remain consistent but there are subtle changes in equilibrium affinity. Kinetic experiments showed that the DNA-protein association is significantly hindered in a crowded environment, but dissociation depends on the size and chemical characteristics of the added molecule. It suggests that surrounding molecules can modify the protein's hydration shell through soft interactions, affecting the protein-ligand binding dynamics and affinity.
SCIENTIFIC REPORTS
(2021)
Article
Physics, Fluids & Plasmas
Piotr Kubala, Michal Ciesla, Bartlomiej Dybiec
Summary: The type of diffusion is influenced by both microscopic dynamics and environmental properties. The presence of a constant drift in a crowded environment increases trapping chances and leads to a more anisotropic diffusion. Individual trajectories are highly variable, impacting the macroscopic properties of the diffusing front. The interplay among drift, diffusion, and a crowded environment results in the emergence of both superdiffusive and subdiffusive patterns in the same system.
Article
Physics, Fluids & Plasmas
Fane Feng, Ting Lei, Nanrong Zhao
Summary: The study uses two-dimensional Langevin dynamics simulations to investigate the effective interactions between passive colloids in a bath with active particles. The results show that factors such as active particle size, crowding-activity coupling, and chirality have significant effects on the attraction or repulsion between particles. As volume fraction increases, the competition between activity and crowding leads to a transition from repulsion to attraction in the effective force.
Article
Robotics
Aamodh Suresh, Angelique Taylor, Laurel D. D. Riek, Sonia Martinez
Summary: This research aims to understand human preferences and behaviors in risky and crowded environments, specifically in navigational settings. The study shows that individuals have diverse path preferences ranging from risky and urgent to safe and relaxed. It also reveals that self-assessed risk and time-urgency do not correlate with path preferences. Additionally, participants express a high interest in understanding robot intentions and decision-making through various modalities like speech, touchscreen, and gestures. These findings provide crucial insights for the design of explainable AI in robots deployed in risky and crowded environments.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2023)
Article
Robotics
Kuanqi Cai, Weinan Chen, Chaoqun Wang, Hong Zhang, Max Q. -H. Meng
Summary: Mobile robots are increasingly used in large-scale and crowded environments, but localization in such settings is challenging due to sparse landmarks and crowd noise. Additionally, navigating safely while considering human comfort is unreliable. To address this problem, we propose a curiosity-based framework that considers human comfort and crowd density, localization uncertainty, and cost-to-go to the target. The framework involves three parts: distance assessment, Curiosity for Positive Content (CPC), and Curiosity for Negative Content (CNC). Evaluation in large-scale and crowded environments demonstrates that our method can find a feasible path that considers localization uncertainty and avoids crowded areas.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2023)
Article
Multidisciplinary Sciences
Maxime Mistretta, Nicolas Gangneux, Giulia Manina
Summary: Preclinical analysis of drug efficacy is crucial for drug development. Conventional bulk-cell assays lack the ability to accurately assess drug efficacy on individual cells, leading to potential overestimation or rejection of valuable candidates. This study introduces a scalable microfluidic platform based on pneumatic operation, allowing for long-term live-cell imaging and analysis of different drug concentrations simultaneously. Experimental results on mycobacterial cells, including the tubercular pathogen, demonstrate the feasibility of the single-cell dose-response assay. This dynamic in-vitro model provides improved predictions of drug efficacy in clinical settings.
SCIENTIFIC REPORTS
(2022)
Article
Computer Science, Software Engineering
Ruwayda Alharbi, Ondrej Strnad, Laura R. Luidolt, Manuela Waldner, David Kouril, Ciril Bohak, Tobias Klein, Eduard Groeller, Ivan Viola
Summary: This article proposes a new visibility and guidance approach called Nanotilus for exploring crowded three-dimensional structures. Unlike traditional methods, Nanotilus provides an inside-out experience, preserving immersion in virtual reality. The approach combines scene sparsification and camera path planning, and includes additional features such as animation control, textual annotation, and text-to-visualization conversion to enhance the guided tour experience.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Engineering, Electrical & Electronic
Matteo Caruso, Enrico Regolin, Federico Julian Camerota Verdu, Stefano Alberto Russo, Luca Bortolussi, Stefano Seriani
Summary: In this paper, a framework is presented to train neural controllers for differential drive mobile robots using deep reinforcement learning algorithms (DQN and A3C). The training process allows for scaling to multiple compute nodes and shows that the A3C asynchronous training procedure can quickly train neural controllers for navigation in crowded environments and test them on real robots.
Article
Chemistry, Multidisciplinary
Ning Zhang, Wenyan Guan, Shouqi Cui, Nana Ai
Summary: This study investigates how complex and crowded intracellular environments affect the conformational rearrangement of metamorphic proteins, revealing that crowded agents primarily impact the exchange rate of XCL1 on a timescale of seconds, but have a slight impact on the exchange rate of KaiB on a timescale of hours. NMR spectroscopy is used to quantify the kinetics and thermodynamics of the switch.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Tom Hoefken, Christian Strauch, Stefanie Schneider, Andrea Scotti
Summary: Particle size disparities can inhibit crystallization, but soft deformable nanogels have the ability to change the size of larger particles and crystallize even with high initial size-polydispersity. Experimental results using neutron scattering with contrast variation show an increase in the parameter describing size-polydispersity for individual nanogels in crowded environments, which is often interpreted as deformation. Computer simulations confirm this qualitative increase of the parameter with increasing particle deformation. Furthermore, the analysis reveals that the size disparities between nanogels do not significantly increase, but their shapes vary greatly.
Review
Biochemistry & Molecular Biology
Erika Kovacs, Julie Anne Zorn, Yongjian Huang, Tiago Barros, John Kuriyan
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 84
(2015)
Article
Biochemistry & Molecular Biology
Erika Kovacs, Rahul Das, Qi Wang, Timothy S. Collier, Aaron Cantor, Yongjian Huang, Kathryn Wong, Amar Mirza, Tiago Barros, Patricia Grob, Natalia Jura, Ron Bose, John Kuriyan
MOLECULAR AND CELLULAR BIOLOGY
(2015)
Article
Cell Biology
Vladislav Belyy, Max A. Schlager, Helen Foster, Armando E. Reimer, Andrew P. Carter, Ahmet Yildiz
NATURE CELL BIOLOGY
(2016)
Article
Biology
Yongjian Huang, Shashank Bharill, Deepti Karandur, Sean M. Peterson, Morgan Marita, Xiaojun Shi, Megan J. Kaliszewski, Adam W. Smith, Ehud Y. Isacoff, John Kuriyan
Review
Biochemistry & Molecular Biology
Vladislav Belyy, Ahmet Yildiz
Article
Biochemistry & Molecular Biology
Mark A. DeWitt, Caroline A. Cypranowska, Frank B. Cleary, Vladislav Belyy, Ahmet Yildiz
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2015)
Article
Multidisciplinary Sciences
Vladislav Belyy, Nathan L. Hendel, Alexander Chien, Ahmet Yildiz
NATURE COMMUNICATIONS
(2014)
Article
Multidisciplinary Sciences
Frank B. Cleary, Mark A. Dewitt, Thomas Bilyard, Zaw Min Htet, Vladislav Belyy, Danna D. Chan, Amy Y. Chang, Ahmet Yildiz
NATURE COMMUNICATIONS
(2014)
Article
Cell Biology
Aylin Goke, Simon Schrott, Arda Mizrak, Vladislav Belyy, Christof Osman, Peter Walter
MOLECULAR BIOLOGY OF THE CELL
(2020)
Article
Multidisciplinary Sciences
Vladislav Belyy, Ngoc-Han Tran, Peter Walter
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biology
Yongjian Huang, Jana Ognjenovic, Deepti Karandur, Kate Miller, Alan Merk, Sriram Subramaniam, John Kuriyan
Summary: Research has shown that the EGFR receptor can adopt different conformations of the extracellular module when binding to different ligands, with implications for intracellular signaling pathways.
Article
Biology
Vladislav Belyy, Iratxe Zuazo-Gaztelu, Andrew Alamban, Avi Ashkenazi, Peter Walter
Summary: Protein folding homeostasis in the endoplasmic reticulum is regulated by the unfolded protein response (UPR), with Inositol-requiring enzyme 1 (IRE1) playing a key role in signal transmission. This study used a two-color single-molecule tracking approach to investigate the oligomerization of IRE1 in live cells. The results suggest that IRE1 exists as a constitutive homodimer and assembles into small oligomers upon ER stress, with its lumenal domain governing the formation of inactive dimers and stress-dependent oligomers.
Article
Biology
Moitrayee Bhattacharyya, Margaret M. Stratton, Catherine C. Going, Ethan D. McSpadden, Yongjian Huang, Anna C. Susa, Anna Elleman, Yumeng Melody Cao, Nishant Pappireddi, Pawel Burkhardt, Christine L. Gee, Tiago Barros, Howard Schulman, Evan R. Williams, John Kurivan