Article
Chemistry, Physical
Bingjie Zhang, Fei Tan, Nanrong Zhao
Summary: This study systematically investigates polymer looping kinetics in active heterogeneous media crowded with a mixture of mobile active particles and immobile obstacles using Langevin dynamics simulations. The results reveal the novel phenomena of inhibition-facilitation transition of the looping rate induced by heterogeneity, crowdedness, and activity, as well as a very non-trivial crowder size effect on the looping kinetics. The underlying mechanism is rationalized by the interplay of polymer diffusion, conformational change, and looping free-energy barrier.
Article
Chemistry, Analytical
Stanko N. Nikolic, Sho Oasa, Aleksandar J. Krmpot, Lars Terenius, Milivoj R. Belic, Rudolf Rigler, Vladana Vukojevic
Summary: Nucleocytoplasmic transport of transcription factors plays a crucial role in cellular function and disease. In this study, we used mpFCS to map the directionality of nucleocytoplasmic transport in live cells and discovered that under ligand-induced translocation, transcription factors are simultaneously transported in and out of the cell nucleus at different locations.
ANALYTICAL CHEMISTRY
(2023)
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)
Article
Physics, Fluids & Plasmas
Su Zhong, Xiaoqun Wu, Yanting Li, Congying Liu
Summary: This paper proposes a metapopulation-like model to investigate the impact of direct and indirect transmissions on susceptible-infected-susceptible-like epidemics on heterogeneous networks. The study also explores disinfection strategies in both spatial and time dimensions. Comparative analysis suggests prioritizing disinfection resource allocation to large-flow environments and timely disinfection of environments with infected visitors.
Article
Business
Nora Jansen, Oliver Hinz
Summary: This study uses digital footprints to identify opinion leaders, finding that what one knows and how active one is are the best predictors.
JOURNAL OF BUSINESS RESEARCH
(2022)
Article
Optics
Peng Gao, G. Ulrich Nienhaus
Summary: The axial line-scanning stimulated emission depletion fluorescence correlation spectroscopy (axial ls-STED-FCS) technique offers higher time resolution through axial line scanning, sub-diffraction spatial resolution, and the ability to study samples with densely labeled membranes.
Article
Biochemistry & Molecular Biology
Muhammad Saqib Sohail, Raymond H. Y. Louie, Zhenchen Hong, John P. Barton, Matthew R. McKay
Summary: This article introduces a method for inferring epistasis and the fitness effects of individual mutations from observed evolutionary histories. Simulations show that this method can accurately infer pairwise epistatic interactions when there is sufficient genetic diversity in the data.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Chemistry, Physical
Kevin J. J. Modica, Ahmad K. K. Omar, Sho C. C. Takatori
Summary: Physical boundaries play a crucial role in governing the transport properties of nearby self-propelled particles. Development of dispersion theories and Brownian dynamics simulations reveal the coupling between surface accumulation and effective diffusivity of active particles in boundary-rich media. Classical models of passive systems fail to capture the impact of unique interplay between activity and microstructure of the internal geometry. A Smoluchowski description of long-time self diffusivity, considering the density and fluctuation fields of active particles, demonstrates the activity-induced slowdown of effective diffusivity.
Article
Engineering, Environmental
Job Augustijn van der Werf, Zoran Kapelan, Jeroen Gerardus Langeveld
Summary: Urban drainage systems can pose ecological and public health risks by releasing untreated contaminated water into the environment. Real-time control combined with rainfall nowcast can effectively reduce pollution loads. This study investigates the accuracy of nowcast data and its impact on the performance of rule-based real-time control procedures. Testing in Rotterdam, the Netherlands, shows that the developed procedures can significantly reduce sewer overflow volumes. However, nowcast data has limitations in accurately quantifying rainfall depths and predicting the end of rainfall events, leading to risks in the control procedures.
WATER SCIENCE AND TECHNOLOGY
(2023)
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
Environmental Sciences
Godwyn-Paulson Pitchamani, Jonathan Muthuswamy Ponniah, Pedro Francisco Rodriguez-Espinosa, Priyadarsi Debajyoti Roy, Juan Manuel Sanchez-Nunez, Lorena Elizabeth Campos Villegas, Francisco Rodriguez-Gonzalez, Ciro Eliseo Marquez-Herrera
Summary: The vertical distribution pattern and concentrations of elements in the studied region were analyzed to understand the origin and pollutant phases of geochemical elements. The sediments in the lagoon exhibited higher concentrations of elements, and the fine-grained fractions played a major role in the concentration and mobilization of metals. The overall assessment indicated that the sediments were unpolluted to moderately polluted, but Cr, Ni, and As could pose potential risks to organisms. Factor analysis revealed the origin and behavior of the studied elements. The study provides valuable insights for the sustainable management of sediment profiles in coastal transitional environments.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Multidisciplinary Sciences
Robert Stelter, Diego Alburez-Gutierrez
Summary: Crowdsourced online genealogies have the potential to reveal population dynamics, but their limitations should be considered. The study found that genealogical coverage is low in the German Empire and high in The Netherlands. In the early 20th century, mortality rates in genealogical data were consistently lower and more homogeneous than in the general population. Prior to the 19th century, mortality rates in genealogical data reflected those of elites in both territories. These findings may be attributed to low coverage and oversampling of elites in online genealogies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
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
Biology
Emeric Bouin, Guillaume Legendre, Yuan Lou, Nichole Slover
Summary: The study suggests that in a two-dimensional heterogeneous environment, the best strategy for populations is to move in one direction only, especially towards the direction with smaller variation in resource distribution. This finding aligns with classical results on the evolution of slow dispersal.
JOURNAL OF MATHEMATICAL BIOLOGY
(2021)
Article
Chemistry, Physical
Dao-Yang Hua, Meng-Bo Luo
Summary: This study investigates the diffusion of polymer chains in a crowded environment with large and small immobile, attractive nanoparticles using Langevin dynamics simulations. The results show that the diffusion of polymer chains is dependent on the distance between nanoparticles and the polydispersity of nanoparticles. At low distances, subdiffusion occurs at high polydispersity, while at large distances, normal diffusion is observed and the diffusion coefficient increases with increasing polydispersity. The study also shows that the disorder of nanoparticles enhances the subdiffusion of polymer chains.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Min Wu, Yi Cui, Amruth Bhargav, Yaroslav Losovyj, Amanda Siegel, Mangilal Agarwal, Ying Ma, Yongzhu Fu
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2016)
Article
Chemistry, Multidisciplinary
Meghan B. Teunis, Katie N. Lawrence, Poulami Dutta, Amanda P. Siegel, Rajesh Sardar
Article
Chemistry, Physical
Min Wu, Amruth Bhargav, Yi Cui, Amanda Siegel, Mangilal Agarwal, Ying Ma, Yongzhu Fu
ACS ENERGY LETTERS
(2016)
Article
Chemistry, Analytical
Ali Daneshkhah, Sudhir Shrestha, Amanda Siegel, Kody Varahramyan, Mangilal Agarwal
Article
Multidisciplinary Sciences
Clement Riedel, Ronen Gabizon, Christian A. M. Wilson, Kambiz Hamadani, Konstantinos Tsekouras, Susan Marqusee, Steve Presse, Carlos Bustamante
Article
Engineering, Environmental
Ali Daneshkhah, Shitiz Vij, Amanda P. Siegel, Mangilal Agarwal
CHEMICAL ENGINEERING JOURNAL
(2020)
Article
Biochemistry & Molecular Biology
Luqi Wang, Yue Wang, Andy Chen, Meghana Teli, Rika Kondo, Aydin Jalali, Yao Fan, Shengzhi Liu, Xinyu Zhao, Amanda Siegel, Kazumasa Minami, Mangilal Agarwal, Bai-Yan Li, Hiroki Yokota
Article
Chemistry, Multidisciplinary
Xiaoju Zhou, Brooke A. Brown, Amanda P. Siegel, Mohamed S. El Masry, Xuyao Zeng, Woran Song, Amitava Das, Puneet Khandelwal, Andrew Clark, Kanhaiya Singh, Poornachander R. Guda, Mahadeo Gorain, Lava Timsina, Yi Xuan, Stephen C. Jacobson, Milos V. Novotny, Sashwati Roy, Mangilal Agarwal, Robert J. Lee, Chandan K. Sen, David E. Clemmer, Subhadip Ghatak
Article
Biochemical Research Methods
M. Woollam, A. P. Siegel, P. Grocki, J. L. Saunders, D. B. Sanders, M. Agarwal, M. D. Davis
Summary: Cystic fibrosis (CF) is a chronic disease characterized by worsening respiratory infections and lung function decline. Pulmonary exacerbations (PEx), episodes of intensified respiratory symptoms, further accelerate the decline in lung function and decrease survival rate. The lack of standard classification for PEx is a challenge and leads to heterogeneous treatments. This study investigated volatile organic compounds (VOCs) in exhaled breath as potential biomarkers for PEx classification and other clinical factors in CF patients. VOCs were analyzed using solid phase microextraction coupled to gas chromatography-mass spectrometry. The results showed that some VOCs correlated with PEx and other clinical variables, suggesting their potential use as biomarkers. VOCs such as 3,7-dimethyldecane, durene, 2,4,4-trimethyl-1,3-pentanediol 1-isobutyrate and 5-methyltridecane were differentially expressed due to PEx. Receiver operator characteristic curves demonstrated the ability of VOCs and lung function measurements to classify PEx. This study highlights the importance of exploring exhaled breath VOCs as biomarkers for CF clinical traits, including PEx, in larger sample cohorts.
JOURNAL OF BREATH RESEARCH
(2022)
Article
Biochemical Research Methods
Mark Woollam, Paula Angarita-Rivera, Amanda P. Siegel, Vikas Kalra, Rajat Kapoor, Mangilal Agarwal
Summary: The expression of volatile organic compounds (VOCs) in the exhaled breath of COVID-19 patients is altered, and analyzing these VOCs can detect COVID-19 infection. Machine learning algorithms can distinguish COVID-19 positive patients from COVID-19 negative patients with high accuracy. After recovery, the VOCs dysregulated by COVID-19 return to baseline levels.
JOURNAL OF BREATH RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Paul Grocki, Mark Woollam, Luqi Wang, Shengzhi Liu, Maitri Kalra, Amanda P. Siegel, Bai-Yan Li, Hiroki Yokota, Mangilal Agarwal
Summary: This study found that volatile organic compounds (VOCs) in mouse urine can accurately and noninvasively predict the efficacy of pitavastatin treatments for breast cancer.
Article
Oncology
Mark Woollam, Amanda P. P. Siegel, Adam Munshi, Shengzhi Liu, Sunil Tholpady, Thomas Gardner, Bai-Yan Li, Hiroki Yokota, Mangilal Agarwal
Summary: Chemometric analyses showed that VOCs in mouse urine were dysregulated by prostate cancer and could distinguish tumor-bearing mice. VOCs in human urine could classify any type of prostate cancer and separate aggressive grades with higher sensitivity and specificity. The overlap in VOC structure and functionality between mice and humans suggests the merit of murine models for identifying biomarker candidates.
Article
Multidisciplinary Sciences
Mark Woollam, Meghana Teli, Paula Angarita-Rivera, Shengzhi Liu, Amanda P. Siegel, Hiroki Yokota, Mangilal Agarwal
SCIENTIFIC REPORTS
(2019)
Article
Biochemical Research Methods
Amanda P. Siegel, Ali Daneshkhah, Dana S. Hardin, Sudhir Shrestha, Kody Varahramyan, Mangilal Agarwal
JOURNAL OF BREATH RESEARCH
(2017)