Article
Biochemical Research Methods
Jianzhao Gao, Shuangjia Zheng, Mengting Yao, Peikun Wu
Summary: This article introduces a new method for estimating solvent accessible area of proteins using deep learning, which achieves high Pearson correlation coefficients on test datasets and outperforms existing estimators. EAGERER is the first method to estimate solvent accessible area using limited information with a deep learning model.
Article
Biochemistry & Molecular Biology
Giulia Babbi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
Summary: By utilizing computational methods, the study explored the physicochemical properties of human huntingtin protein based on the last cryogenic electron microscopy structure, highlighting a mix of hydrophobic and hydrophilic patterns on the protein surface. Exposed residues were found to cluster in specific regions, while remaining portions of the surface may contain calcium-binding sites proposed as potential mediators for protein-membrane interactions. These findings are supported by current knowledge of huntingtin functional annotations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Materials Science, Multidisciplinary
Kseniya Girel, Aliaksandr Burko, Aliaksei Barysiuk, Sergey Dubkov, Dmitry Gromov, Hanna Bandarenka
Summary: We propose a method to identify the time point of Ag particle formation with prominent SERS activity during Ag wet electroless deposition on macro-PS by measuring the decrease in surface potential. The most intense SERS spectra of DTNB were collected on macro-PS covered with Ag particles for 20 minutes. We claim a TNB detection limit of 2 x 10(-9) M by considering the chemisorption of monomolecular TNB layer on the surface of Ag structures. The analytical enhancement factor was calculated to be approximately 0.7 x 10(7).
CURRENT APPLIED PHYSICS
(2023)
Article
Mathematics
Kapil Jaglan, Anbareeswaran Sairam Kaliraj
Summary: It is known that minimal surfaces over convex domains are always globally area-minimizing, but this is not necessarily true for minimal surfaces over non-convex domains. Recently, it was proved that minimal surfaces over a bounded linearly accessible domain D of order beta (0,1) must be globally area-minimizing if a certain geometric inequality is satisfied on the boundary of D. In this article, we provide sufficient conditions for a sense-preserving harmonic function f=h+(g) to be linearly accessible of order beta. We also present a method to construct harmonic polynomials that map the open unit disk |z|<1 onto a linearly accessible domain of order beta. Using these harmonic polynomials, we construct families of globally area-minimizing minimal surfaces over non-convex domains.
JOURNAL OF GEOMETRIC ANALYSIS
(2023)
Article
Engineering, Biomedical
Fanyu Zhang, Haoning Qi, Wenting Mo, Yueqi Ni, Qin Zhao, Yulan Wang, Shuting Jiang, Qinchao Tang, Yihong Cheng, Xiangheng Xiao, Yufeng Zhang
Summary: This study reveals the mechanism of how surface accessible area (SAA), a nanoscale property, affects foreign body reaction (FBR) from the perspective of damage associated molecular patterns (DAMPs), and provides a new direction for designing better biocompatible implants.
ADVANCED HEALTHCARE MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Hazem M. Kotb, Norman E. Davey
Summary: The identification of protein surfaces required for interaction with other biomolecules broadens our understanding of protein function and their regulation, as well as the impact of disease mutations. This study introduces tools to identify conserved surfaces on AlphaFold2 structural models, resulting in the discovery of numerous uncharacterized yet highly conserved surfaces in the human proteome.
Article
Chemistry, Multidisciplinary
Fanqi Qin, Md. Fahim Salek, Parisa Asadi, Lauren E. Beckingham
Summary: This study aims to quantitatively assess the evolution of accessible mineral surface area in porous media for a multimineralic system undergoing mineral dissolution reactions induced by acid exposure. Results show an overall increase in total surface area due to the reaction; however, individual mineral surface areas may increase or decrease. The evolution of mineral surface area is largely impacted by the total surface area as well as the pore connectivity rather than porosity and volume fraction evolution.
ACS EARTH AND SPACE CHEMISTRY
(2023)
Article
Geochemistry & Geophysics
Jin Ma, Mehrdad Ahkami, Martin O. Saar, Xiang-Zhao Kong
Summary: The accessible surface areas (ASAs) of rock-forming minerals play a fundamental role in mineral reactivity with formation fluids, with efficiency varying significantly based on fluid chemistry and flow characteristics. A novel joint method for calculating ASAs of individual minerals in sandstone was developed and used to investigate the impact of flow rate on ASA efficiency during mineral dissolution reactions. The study found that dolomite reactivity increased with flow rate, reaching a relatively stable value, and compared two methods for analyzing experimental observations, highlighting the importance of careful consideration of flow rate when interpreting results.
Article
Chemistry, Multidisciplinary
Yu Tian, Aiji Wang, Yaqing Wei, Minghui Pei, Rongrong Cao, Zhenao Gu, Qi Yuan, Yiwen Hu, Jing Wang, Kunhui Liu, Dashan Shang, Jiebin Niu, Xiaoqiang An, Run Long, Jinxing Zhang
Summary: This study demonstrates a controllable water splitting reaction by constructing a hydroxyls-bonded surface on a ferroelectric material. The up-shift of band edge positions at this surface enhances the transfer of holes and electrons, leading to enhanced oxygen or hydrogen evolutions, respectively. Additionally, the introduction of ferroelectric super-domains with electric fields improves the separation of photogenerated carriers, resulting in a significant increase in photocurrent.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Physics, Multidisciplinary
Huseyin Ozan Tekin, Ghada ALMisned, Shams A. M. Issa, Emel Serdaroglu Kasikci, Mahreen Arooj, Antoaneta Ene, M. S. Al-Buriahi, Muhsin Konuk, Hesham M. H. Zakaly
Summary: This study examined the chemical and physical characteristics of several flavonoid compounds and found that their elemental compositions have a direct effect on their properties. Saponarin showed the highest polar surface area, solvent accessible surface area, stability, and gamma-ray attenuation characteristics across a broad photon energy range.
FRONTIERS IN PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Fanqi Qin, Md. Fahim Salek, Parisa Asadi, Chidera Iloejesi, Olivia Brunhoeber, Mukseet Mahmood, Lauren E. Beckingham
Summary: The quantification of mineral reactive surface area varies significantly depending on the method used, leading to discrepancies in reactive transport models. This study explores the possibility of estimating mineral accessible surface areas (ASAs) from easily measured properties like mineral abundance and porosity. The results show that mineral accessibility can be predicted based on these properties, reducing the need for extensive image analysis.
ACS EARTH AND SPACE CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Fanqi Qin, Md. Fahim Salek, Parisa Asadi, Chidera Iloejesi, Olivia Brunhoeber, Mukseet Mahmood, Lauren E. Beckingham
Summary: This study explores the possibility of estimating mineral accessible surface areas (ASAs) from easily measured properties, such as mineral abundance and porosity. Comparing properties such as mineral accessibility, mineral ASAs, connected porosity, and clay content, it was observed that feldspar mineral accessibility generally increases with increasing abundance, while quartz accessibility decreases with increasing clay content. Quantitative observations and predictive relationships for ASAs from porosity and mineral volume fraction are developed to reduce the required extent of image analysis.
ACS EARTH AND SPACE CHEMISTRY
(2023)
Article
Nanoscience & Nanotechnology
Jamie Cuchiaro, Jacob DeRoo, Jon Thai, Melissa M. Reynolds
Summary: In this study, the suitability of a commercially available metal-organic framework (MOF) called MIL-53(Al) as a stationary phase for cannabinoid separations was evaluated. The results showed that most of the MOF surface area was inaccessible for adsorption by cannabinoids due to size-exclusion effects. This study suggests that MOFs may have an upper limit for the size of the analyte and may be more suitable for separations in the gas phase.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Multidisciplinary
Xiao Sun, Qiang Li, Daxian Cao, Ying Wang, Alexander Anderson, Hongli Zhu
Summary: A newly designed N-doped carbon fiber with micropores on its surface has been shown to significantly improve the electrochemical performance of all-solid-state lithium-sulfur batteries, enhancing the contact between sulfur and solid electrolyte while providing excellent electrical conductivity. This structurally designed carbon fiber boosts the initial capacity, cycling stability, and rate capability of the batteries, demonstrating a promising potential for practical applications in energy storage systems.
Review
Biochemistry & Molecular Biology
Tomoki Naito, Yasunori Saheki
Summary: This study discusses the importance of accessible cholesterol in cells and how the endoplasmic reticulum monitors the cholesterol levels on the plasma membrane. It highlights the role of GRAMD1s proteins in facilitating the transport of cholesterol from the plasma membrane to the ER.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2021)
Article
Chemistry, Multidisciplinary
Tobias Voepel, Rebecca Scholz, Luca Davico, Magdalena Gross, Steffen Buening, Sabine Kareth, Eckhard Weidner, Simon Ebbinghaus
CHEMICAL COMMUNICATIONS
(2015)
Article
Biophysics
Tobias Voepel, En Ning Saw, Volker Hartmann, Rhodri Williams, Frank Mueller, Wolfgang Schuhmann, Nicolas Plumere, Marc Nowaczyk, Simon Ebbinghaus, Matthias Roegner
Meeting Abstract
Biophysics
Thomas-Otavio Peulen, Carola S. Hengstenberg, Ralf Biehl, Mykola Dimura, Alessandro Valeri, Semra Ince, Tobias Voepel, Bela Farago, Holger Gohlke, Christian Herrmann, Johann Klare, Andreas Stadler, Claus A. M. Seidel
BIOPHYSICAL JOURNAL
(2016)
Article
Biophysics
Tobias Voepel, En Ning Saw, Volker Hartmann, Rhodri Williams, Frank Mueller, Wolfgang Schuhmann, Nicolas Plumere, Marc Nowaczyk, Simon Ebbinghaus, Matthias Roegner
Article
Chemistry, Multidisciplinary
Tobias Voepel, Kenny Bravo-Rodriguez, Sumit Mittal, Shivang Vachharajani, David Gnutt, Abhishek Sharma, Anne Steinhof, Oluwaseun Fatoba, Gisa Ellrichmann, Michael Nshanian, Christian Heid, Joseph A. Loo, Frank-Gerrit Klaener, Thomas Schrader, Gal Bitan, Erich E. Wanker, Simon Ebbinghaus, Elsa Sanchez-Garcia
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2017)
Article
Chemistry, Physical
Steffen Buening, Abhishek Sharma, Shivang Vachharajani, Estella Newcombe, Angelique Ormsby, Mimi Gao, David Gnutt, Tobias Voepel, Danny M. Hatters, Simon Ebbinghaus
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2017)
Article
Multidisciplinary Sciences
Rebecca J. Wood, Angelique R. Ormsby, Mona Radwan, Dezerae Cox, Abhishek Sharma, Tobias Voepel, Simon Ebbinghaus, Mikael Oliveberg, Gavin E. Reid, Alex Dickson, Danny M. Hatters
NATURE COMMUNICATIONS
(2018)
Article
Biochemistry & Molecular Biology
Tobias Voepel, Carola S. Hengstenberg, Thomas-Otavio Peulen, Yathrib Ajaj, Claus A. M. Seidel, Christian Herrmann, Johann P. Klare
Article
Multidisciplinary Sciences
Tobias Voepel, George I. Makhatadze
Article
Instruments & Instrumentation
C. Rumancev, A. Grafenstein, T. Vopel, S. Stuhr, A. R. von Gundlach, T. Senkbeil, A. J. Garrevoet, L. Jolmes, B. Konig, C. Falkenberg, S. Ebbinghaus, W. H. Schroeder, A. Rosenhahn
JOURNAL OF SYNCHROTRON RADIATION
(2020)
Article
Chemistry, Multidisciplinary
Andreas Graefenstein, Christoph Rumancev, Roland Pollak, Benjamin Haemisch, Vanessa Galbierz, Walter H. Schroeder, Jan Garrevoet, Gerald Falkenberg, Tobias Voepel, Klaus Huber, Simon Ebbinghaus, Axel Rosenhahn
Summary: Protein aggregation is a characteristic of severe neurodegenerative disorders, and metal ions play a significant role in this process. Through analysis, it was found that the zinc content in cells increased threefold and the potassium enrichment increased tenfold, which may be a result of cellular stress response. Although the ion content in aggregate-containing cells differs from non-aggregate-containing cells, there is no difference in ion content at the location of intracellular inclusion bodies. These results suggest that changes in ion concentration are not exclusively linked to the formation of specific proteins.
Article
Chemistry, Multidisciplinary
Christoph Rumancev, Tobias Voepel, Susan Stuhr, Andreas R. Gundlach, Tobias Senkbeil, Markus Osterhoff, Michael Sprung, Vasil M. Garamus, Simon Ebbinghaus, Axel Rosenhahn
Summary: Huntington's disease is a neurodegenerative disorder associated with the extension of polyglutamine in proteins, leading to the formation of amyloidal structures. By using nanoprobe small angle X-ray scattering in cellulo, the structure of Htt amyloid fibrils was investigated under cryogenic conditions, providing insights into aggregate formation without chemical fixation. It was also revealed that nanoprobe cryo-SAXS can serve as a powerful tool to study the kinetics of amyloid aggregate formation inside cells and understand how fibril formation can be influenced by drugs and external stimuli.
Meeting Abstract
Biophysics
Tobias Voepel, Daniel Klose, Carola-Sophie Hengstenberg, Heinz-Juergen Steinhoff, Christian Herrmann, Johann P. Klare
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2011)
Article
Biophysics
Christoph Rumancev, Tobias Voepel, Susan Stuhr, Andreas von Gundlach, Tobias Senkbeil, Simon Ebbinghaus, Jan Garrevoet, Gerald Falkenberg, Bjoern De Samber, Laszlo Vincze, Axel Rosenhahn, Walter Schroeder
Summary: X-ray fluorescence analysis enables the study of trace element distributions in biological specimens under cryogenic conditions. The system described in this work was applied to analyze the elemental distribution in single HeLa cells.
Article
Biochemistry & Molecular Biology
Michael Dirkmann, Javier Iglesias-Fernandez, Victor Munoz, Pandian Sokkar, Christoph Rumancev, Andreas von Gundlach, Oktavian Krenczyk, Tobias Voepel, Julia Nowack, Martin A. Schroer, Simon Ebbinghaus, Christian Herrmann, Axel Rosenhahn, Elsa Sanchez-Garcia, Frank Schulz
