Article
Biochemistry & Molecular Biology
Huayin Bao, Wei Wang, Haibo Sun, Jianzhong Chen
Summary: This study explores the effect of mutations D33K, A59T, and L120A on the conformation states of GDP-bound HRAS using Gaussian accelerated molecular dynamics (GaMD) simulations and constructions of free energy landscapes (FELs). The results suggest that mutations alter the flexibility and motion modes of the switch domains in HRAS, leading to more disordered states and affecting GDP-HRAS interactions. The study reveals the importance of salt bridges and hydrogen bonding interactions (HBIs) in the binding of GDP to HRAS and highlights the instability of magnesium ions and GDP interactions with the switch SI in causing extreme disorder. This work provides insights into the energetic basis and molecular mechanism of HRAS function.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Forestry
Xinwang Wang, Warren Chatwin, Angelyn Hilton, Keith Kubenka
Summary: This study analyzed over 400 samples of Carya species and their hybrids from the USDA National Collection of Genetic Resources for Carya using nuclear and plastid microsatellite markers. The results showed clear taxonomic classifications at multiple levels and patterns of interspecific hybridity. The markers were found to be useful in examining and characterizing populations and hybrids in the genus Carya, and may contribute to pecan breeding programs and the identification of pecan trees for growers.
Article
Chemistry, Physical
Talant Ruzmetov, Ruben Montes, Jianan Sun, Si-Han Chen, Zhiye Tang, Chia-en A. Chang
Summary: Understanding ligand binding kinetics and thermodynamics is crucial in chemical and biomedical research. We developed a Binding Kinetics Toolkit (BKiT) that can analyze trajectories and compute free energy and kinetics profiles. BKiT uses principal component space to generate approximated coordinates and implements milestoning theory to construct free energy profiles and estimate binding residence time.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Energy & Fuels
Akbar Saba, Nepu Saha, Keenan-Conrad Williams, Charles J. Coronella, M. Toufiq Reza
Summary: This study investigated the effects of torrefaction temperature, pelletization temperature, and pelletization pressure on the energy density of torrefied char pellets using multivariate analyses and multivariate linear regression. The statistical analysis showed that all independent parameters are statistically significant for energy density, and the regression analysis indicated that mass density, higher heating value, and energy density have the highest output predictability.
BIOMASS CONVERSION AND BIOREFINERY
(2022)
Article
Engineering, Biomedical
Hui Zhou, Janny Pineiro Llanes, Malisa Sarntinoranont, Ghatu Subhash, Chelsey S. Simmons
Summary: The study established a method to determine the alignment of proteins in soft tissues using polarized Raman spectroscopy (PRS), which offers non-destructive, label-free sample preparation, and developed an Amplitude Alignment Metric for evaluation. The research found that this method provides a high level of alignment in soft tissues.
ACTA BIOMATERIALIA
(2021)
Article
Nanoscience & Nanotechnology
Valentin Aubriet, Kristell Courouble, Olivier Bardagot, Renaud Demadrille, Lukasz Borowik, Benjamin Grevin
Summary: In this study, the authors used pump-probe Kelvin probe force microscopy (pp-KPFM) and non-contact atomic force microscopy (nc-AFM) under ultrahigh vacuum to investigate the nature of light-induced surface potential dynamics in alumina-passivated crystalline silicon and an organic bulk heterojunction thin film. They found two different kinds of photo-induced charge distributions that give rise to potential shifts with opposite polarities, each characterized by different dynamics.
Article
Multidisciplinary Sciences
Anika Kueken, Damoun Langary, Zoran Nikoloski
Summary: Understanding the complexity of metabolic networks can be characterized by identifying multi-reaction dependencies. Concordant complexes can capture these dependencies and reduce the apparent complexity of metabolic networks. The metabolic network of Escherichia coli is more tightly coordinated than expected by chance.
Article
Automation & Control Systems
Oxana Rodionova, Sergey Kucheryavskiy, Alexey Pomerantsev
Summary: This paper introduces new tools for exploration and interpretation of PCA results, discussing important aspects of high dimensional datasets and presenting new methods for assessing PCA model complexity. Through simulated and real-world examples, the application capabilities of these tools are demonstrated.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2021)
Article
Computer Science, Artificial Intelligence
Qin Tao, Yajing Si, Fali Li, Peiyang Li, Yuqin Li, Shu Zhang, Feng Wan, Dezhong Yao, Peng Xu
Summary: This study revealed the dynamic process of decision response and feedback in gambling, showing that different decisions and feedback lead to distinct brain network activities.
INTERNATIONAL JOURNAL OF NEURAL SYSTEMS
(2021)
Article
Chemistry, Multidisciplinary
Wioletta Biel, Urszula Pomietlo, Robert Witkowicz, Ewa Piatkowska, Aneta Kopec
Summary: The study aimed to evaluate the composition, polyphenolic content, and antioxidant activity of 27 plant materials collected in West Pomeranian, Poland. Chemical composition was determined using official methods, and antioxidant activity was tested using different methods. The highest dry matter concentration was found in milk thistle and black cumin, while the lowest was found in black chokeberry. Garlic, stinging nettle, and cleavers had the highest polyphenolic content and antioxidant activity. Further research is needed to identify potentially harmful compounds.
APPLIED SCIENCES-BASEL
(2023)
Article
Genetics & Heredity
Souhir Mestiri, Sami Boussetta, Andrew J. Pakstis, Sarra Elkamel, Amel Ben Ammar Elgaaied, Kenneth K. Kidd, Lotfi Cherni
Summary: The study evaluated the genetic diversity of seven North African populations, revealing that the Smar population has a unique genetic structure and higher allelic frequencies possibly due to isolation, endogamy, and genetic drift. Additionally, the genetic diversity of North African populations is similar to African and European populations, with a significant Eurasian genetic component.
Article
Multidisciplinary Sciences
Andrew Wheat, Clinton Yu, Xiaorong Wang, Anthony M. Burke, Ilan E. Chemmama, Robyn M. Kaake, Peter Baker, Scott D. Rychnovsky, Jing Yang, Lan Huang
Summary: A robust in vivo XL-MS platform has been developed to map protein-protein interactions at a systems level, enabling the construction of the largest in vivo PPI network to date from HEK 293 cells. This advanced strategy provides a highly detailed panoramic portrait of human interactomes associated with diverse cellular pathways and can be generalized for charting protein interaction landscapes in any organisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Engineering, Civil
Aleksandar Aksentijevic, Dragutin T. Mihailovic, Anja Mihailovic, Vijay P. Singh
Summary: This study applied a new complexity measurement to investigate the spatiotemporal regularities of monthly streamflow in Bosnia and Herzegovina, revealing its hydrological effects. The results demonstrate that this method is an effective tool for uncovering data patterns that cannot be captured by KC and other complexity measures.
JOURNAL OF HYDROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Anita Kumari, Lovika Mittal, Mitul Srivastava, Dharam Pal Pathak, Shailendra Asthana
Summary: The activation process of FXR is regulated by the synergy between agonists and co-activators, with conformational dynamics playing a crucial role in achieving the bioactive state. Insights into the interplay of agonists and co-activators revealed significant differences in molecular bonding patterns within the ligand binding domain of FXR, ultimately influencing the structural anomalies in different FXR systems. Understanding the critical residue positioning during conformational changes and the modulation occurring in FXR provides valuable information for rational design of its agonists.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Development Studies
Richard Fischer, Fabian Tamayo Cordero, Tatiana Ojeda Luna, Ruben Ferrer Velasco, Maria DeDecker, Bolier Torres, Lukas Giessen, Sven Guenter
Summary: Governance elements act conjointly and contribute to the reduction of deforestation, particularly elements such as land tenure and participation. Performance-oriented decisions focusing on selected governance elements can lead to improved outcomes in forest management.
Article
Physics, Multidisciplinary
Norbert Schaudinnus, Bjoern Bastian, Rainer Hegger, Gerhard Stock
PHYSICAL REVIEW LETTERS
(2015)
Article
Chemistry, Physical
Alexandros Altis, Moritz Otten, Phuong H. Nguyen, Rainer Hegger, Gerhard Stock
JOURNAL OF CHEMICAL PHYSICS
(2008)
Article
Chemistry, Physical
Rainer Hegger, Gerhard Stock
JOURNAL OF CHEMICAL PHYSICS
(2009)
Article
Chemistry, Physical
Norbert Schaudinnus, Andrzej J. Rzepiela, Rainer Hegger, Gerhard Stock
JOURNAL OF CHEMICAL PHYSICS
(2013)
Article
Chemistry, Physical
Andrzej J. Rzepiela, Norbert Schaudinnus, Sebastian Buchenberg, Rainer Hegger, Gerhard Stock
JOURNAL OF CHEMICAL PHYSICS
(2014)
Article
Chemistry, Physical
Ruibin Liang, Stephen J. Cotton, Robert Binder, Rainer Hegger, Irene Burghardt, William H. Miller
JOURNAL OF CHEMICAL PHYSICS
(2018)
Article
Chemistry, Physical
Rainer Hegger, Robert Binder, Irene Burghardt
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Article
Chemistry, Physical
Gabriele D'Avino, Rainer Hegger, Dominik Brey, Praveen K. Budakoti, Stephane Mery, Irene Burghardt
Summary: This study investigates the electron-hole separation in self-assembled nanoscale structures composed of donor-acceptor co-oligomers and reveals the differences in electron and hole transport. Based on the atomistic structure obtained by electron diffraction and microelectrostatics analysis, the rates of electron-hole separation and dissociation yield can be computed using kinetic Monte Carlo simulations.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Physical
Alexandros Altis, Phuong H. Nguyen, Rainer Hegger, Gerhard Stock
JOURNAL OF CHEMICAL PHYSICS
(2007)
Article
Physics, Multidisciplinary
Rainer Hegger, Alexandros Altis, Phuong H. Nguyen, Gerhard Stock
PHYSICAL REVIEW LETTERS
(2007)
Article
Physics, Fluids & Plasmas
L Matassini, H Kantz, J Holyst, R Hegger
Article
Engineering, Electrical & Electronic
R Hegger, H Kantz, L Matassini
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS I-FUNDAMENTAL THEORY AND APPLICATIONS
(2001)
Article
Mathematics, Interdisciplinary Applications
RP Kapsch, H Kantz, R Hegger, M Diestelhorst
INTERNATIONAL JOURNAL OF BIFURCATION AND CHAOS
(2001)
Article
Physics, Multidisciplinary
G Giacomelli, R Hegger, A Politi, M Vassalli
PHYSICAL REVIEW LETTERS
(2000)