Article
Chemistry, Physical
Felix Mayr, Milan Harth, Ioannis Kouroudis, Michael Rinderle, Alessio Gagliardi
Summary: This Perspective discusses the potential of novel machine learning techniques in exploring optoelectronic materials, and their application in accelerating calculations and providing experimental guidance. It also outlines the prospects of machine-learned molecular dynamics potentials, physically informed neural networks, and generative methods based on existing work.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Hengyi Xie, Ana Rojas, Gia G. Maisuradze, George Khelashvili
Summary: This study investigates the key steps in Aβ fibril elongation, using molecular dynamics simulations to study the lock phase process in detail. Through analysis of the simulation trajectories, a key intermediate state was discovered in which a hairpin structure forms, exerting significant influence on the lock phase of fibril elongation. The findings reveal a molecular mechanism for the facilitation of Aβ fibril elongation by amyloidogenic hydrophobic patches.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Shintaro Sugiura, Yuki Shintani, Daisuke Mori, Sayuri L. Higashi, Aya Shibata, Yoshiaki Kitamura, Shin-ichiro Kawano, Koichiro M. Hirosawa, Kenichi G. N. Suzuki, Masato Ikeda
Summary: The artificial construction of multicomponent supramolecular materials has attracted attention due to their orthogonally assembled architectures. In this study, we combined peptide-based self-assembled fibrous nanostructures with globular DNA nanoflowers to develop unique hybrid materials. Fluorescence imaging was used to dissect the orthogonally constructed architectures. By utilizing the distinct functions of peptides and DNA, these materials show promising opportunities for bioapplications as a soft matrix.
Article
Chemistry, Applied
Takayuki Kono, Kaoru Adachi, Yasuhisa Tsukahara
Summary: The morphology of graft block copolymers on the substrate can be controlled by designing side chains using segment affinities to the substrate.
REACTIVE & FUNCTIONAL POLYMERS
(2022)
Article
Chemistry, Physical
Rahul Sahu, Divya Nayar
Summary: This study investigates the effects of chemical nature and soft attractive energy of crowders on water-mediated hydrophobic interactions between non-polar solutes using molecular dynamics simulations. The results show that different types of crowders have varying effects on hydrophobic interactions, with small-sized crowders primarily driving the interaction through an entropic depletion effect, and bulky crowders strengthening it through preferential interactions with the solute. The findings suggest that both entropic and energetic effects play crucial roles in determining hydrophobic associations.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Zhen Yang, Lina Zhao, Min Hu, Di Cai, Ziqi Tian, Jan Baeyens, Raf Dewil, Peiyong Qin, Weiben Yang, Nigel J. D. Graham
Summary: Researchers have successfully developed high-performance nanoflocculants that can remove multiple contaminants from water, improve the structural and dewatering properties of flocs, and reduce the environmental risks associated with metal leaching.
Article
Construction & Building Technology
Yifan Liu, Ran Gao, Zhiheng Zhang, Wenle Zhu, Lei Zhou, Ruoyin Jing, Qiang Zheng, Angui Li
Summary: This paper investigates the resistance reduction mechanism of bends in ventilation and air conditioning duct systems, proposing a novel low-resistance bend design with a tongue-shaped guide vane. Through experiments and numerical simulations, it is demonstrated that the bend with a tongue-shaped guide vane has a significantly higher resistance reduction effect compared to traditional vanes, with the best performance achieved when the aspect ratio is close to 1.0, resulting in a reduction of up to 31% in resistance.
BUILDING AND ENVIRONMENT
(2021)
Article
Chemistry, Physical
Khatereh Azizi, Alessandro Laio, Ali Hassanali
Summary: Through advanced data analysis techniques, researchers characterized the shape of voids surrounding model polymers in water. The voids were found to be rough even when the polymer is folded, with branches extending over 1 nm away. When the voids surround particles with a radius similar to 1 nm, they start to resemble the quasispherical shape predicted by dewetting theory, providing insights into vapor-like interfaces underlying dewetting transitions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Jessi E. S. van der Hoeven, Jelena Jelic, Liselotte A. Olthof, Giorgio Totarella, Relinde J. A. van Dijk-Moes, Jean-Marc Krafft, Catherine Louis, Felix Studt, Alfons van Blaaderen, Petra E. de Jongh
Summary: The study investigates the performance of an Au-Pd core-shell catalyst in the selective hydrogenation of butadiene, showing shell-thickness-dependent catalytic activity, high selectivity, and activity up to 50 times greater than that of alloyed counterparts.
Article
Chemistry, Physical
Nabankur Dasgupta, Tuan A. Ho, Susan B. Rempe, Yifeng Wang
Summary: Understanding the formation of H2CO3 in water from CO2 is crucial in environmental and industrial processes. This study reveals significant differences in the free energy and reaction characteristics between bulk and nanoconfined water. Nanoconfinement not only lowers the energy barrier, but also alters the reaction from endothermic to exothermic. The stronger solvation and improved proton transfer under nanoconfinement enhance the reaction's thermodynamics and kinetics.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Computer Science, Artificial Intelligence
Hiroyuki Kambara, Atsushi Takagi, Haruka Shimizu, Toshihiro Kawase, Natsue Yoshimura, Nicolas Schweighofer, Yasuharu Koike
Summary: The study introduced a model to control free reaching movements and demonstrated good adaptability in force field adaptation tasks, consistent with reported behavioral phenomena. The model can adjust the endpoint's equilibrium position and force modulation, generating fast and slow learning processes. Without the need for desired trajectories, it can predict force generation patterns by exploring the environment.
Article
Chemistry, Multidisciplinary
Gabriela Jajko, Sofia Calero, Pawel Kozyra, Waclaw Makowski, Andrzej Slawek, Barbara Gil, Juan Jose Gutierrez-Sevillano
Summary: This study demonstrates that introducing defects to UiO-66 alters its nature from hydrophobic to hydrophilic, affecting the adsorption mechanism of polar and non-polar molecules, based on a combination of theoretical and experimental approaches.
COMMUNICATIONS CHEMISTRY
(2022)
Article
Optics
Seok Hyung Lie, Nelly H. Y. Ng
Summary: This study investigates whether catalysts used in quantum resource theories are affected by external systems and whether such correlations are beneficial or detrimental to catalysis, and if the classicality or quantumness of these correlations matter. By examining the repeatability of measurement outcomes, it is found that systems quantumly correlated with an external system exhibit the same property against general quantum channels. These results demonstrate that only classical correlations enable catalysis.
Article
Chemistry, Physical
Morten Ledum, Samiran Sen, Sigbjorn Loland Bore, Michele Cascella
Summary: Hybrid particle-field molecular dynamics is a molecular simulation strategy that couples particles to a density field. The Hamiltonian hybrid particle-field method has been expanded and generalized to establish compatibility with any local soft pair potential. The mean-field regime observed in hybrid particle-field simulations is determined by the systems considered, and the Hamiltonian hybrid particle-field model has been shown to effectively capture all properties of the Gaussian Core model.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Shaohua Zhang, Wei Li, Jiabin Luan, Abhinav Srivastava, Vincenzo Carnevale, Michael L. Klein, Jiawei Sun, Danni Wang, Serena P. Teora, Sjoerd J. Rijpkema, Johannes D. Meeldijk, Daniela A. Wilson
Summary: Researchers report an adaptive non-covalent binding strategy for surface functionalization using a hydrophobic anchor to insert into a poly(ethylene glycol) (PEG) host. This strategy allows for spontaneous loading of hydrophilic charged and non-charged functional modules onto the PEG surface without the need for catalysts or binding groups. The reversible insertion of the hydrophobic anchor enables programmable surface functionalization, challenging the current understanding of PEG in hydrophilicity and potentially advancing nanomedicine, advanced materials, and nanotechnology.
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Krzysztof Gadek, Tomasz Gubala, Piotr Nowakowski, Piotr Fabian, Leszek Konieczny
Summary: This study characterized the structures of water-soluble proteins and membrane proteins using the fuzzy oil drop model. The analysis aimed to verify the potential use of an external force field in simulating the protein-folding process while considering the diverse nature of the environment that ensures a biologically active structure.
Article
Neurosciences
Werner Sommer, Katarzyna Stapor, Grzegorz Konczak, Krzysztof Kotowski, Piotr Fabian, Jeremi Ochab, Anna Beres, Grazyna Slusarczyk
Summary: This article introduces a new method (RESPERM) for detecting a single changepoint in a linear time series regression model. The study found that RESPERM detected changepoints with lower variance in time series with medium to large amounts of noise compared to the well-established SEGMENTED method. In practical applications, RESPERM is suitable for datasets with high noise levels.
Article
Biochemical Research Methods
Irena Roterman, Adam Sieradzan, Katarzyna Stapor, Piotr Fabian, Patryk Wesolowski, Leszek Konieczny
Summary: In computer simulations of protein folding, a module representing a polar solvent in water form was introduced. This module implements the fuzzy oil drop model (FOD), which uses a 3D Gauss function to express the presence of a polar environment and guide the folding process towards a hydrophobic core. Simulations using this model showed the presence of a hydrophobic core in the protein structures, even where it was absent in the native structure. The proposed modified FOD model (FOD-M) explains this phenomenon and highlights the importance of considering factors other than polarity in the folding environment.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Piotr Fabian, Leszek Konieczny
Summary: This article investigates the structure and function of Connexins and pannexins proteins. Through comparative analysis, it is found that their hydrophobicity distribution and external force field characteristics are different, thus affecting their activity in different environments.
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Dawid Dulak, Leszek Konieczny
Summary: The experimentally determined structures of amyloid forms are primarily characterized by the two-dimensional forms of a single polypeptide chain, which is made possible by the beta structure and the numerous hydrogen bonds. This study proposes a possible mechanism for obtaining such a structure based on the geometric characterization of the polypeptide chain and molecular dynamics results. The potential mechanism of amyloid transformation is presented using transthyretin and amyloid A beta as examples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Irena Roterman, Katarzyna Stapor, Piotr Fabian, Leszek Konieczny
Summary: This paper analyzes the structure of the hydrophobic core in a collection of intrinsically disordered proteins (IDPs) and proposes an alternative classification method for intrinsically disordered regions (IDR) based on the ordering of the hydrophobic core.
Article
Multidisciplinary Sciences
Mateusz Banach
Summary: This paper demonstrates, discusses, and compares the effects of symmetrization in two calculation subroutines of the Fuzzy Oil Drop model for protein hydrophobicity density. The proposed modifications improve the accuracy, robustness, speed, and usability of the model, as confirmed by tests on various molecules with different shapes and functions.
Article
Engineering, Biomedical
Krzysztof Kotowski, Jeremi Ochab, Katarzyna Stapor, Werner Sommer
Summary: The study aims to assess the impact of ocular artifact removal on the single-trial N250 ERP analysis of face learning. By introducing a new semi-automatic approach, ocular artifact filtration significantly improved the regression modeling of single-trial ERP amplitudes, which is of great significance for the conclusions about the face learning process in individual participants.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2023)
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Leszek Konieczny
Summary: The amyloid structures in the PDB database are compared with their wild type forms. Amyloid fibrils have a 2D structure and a different hydrogen bond network compared to globular proteins. The beta-structure segments in amyloid fibrils have an anti-parallel system of hydrogen bonds. The conformational analysis of Phi and Psi angles reveals the presence of specific conditions and the correlation coefficient can indicate the distribution on the Ramachandran map.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Krzysztof Kotowski, Piotr Fabian, Irena Roterman, Katarzyna Stapor
Summary: Protein secondary structure prediction is crucial for understanding protein structure and function. The ProteinUnetLM model, based on a convolutional Attention U-Net architecture, achieves high prediction quality and inference times comparable to the best LSTM-based models without the need for time-consuming calculations. It outperforms LSTM-based predictors and shows potential for advancing the field.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Leszek Konieczny
Summary: Proteins transporting ions or molecules across the cell membrane play vital roles in maintaining stability and performing biological functions. The hydrophobicity distribution of structures in In and Out conformations affects their stability and conformational changes.
Article
Physics, Multidisciplinary
Irena Roterman, Leszek Konieczny
Summary: Interpreting biological phenomena at the molecular and cellular levels reveals the ways in which information that is specific to living organisms is processed. This paper describes the quantitative relations that characterize information during the successive steps of the biological dogma, illustrating a transition from the recording of information in a DNA strand to the production of proteins exhibiting a defined specificity. The purpose of this paper is the analysis of information flow in organisms with a particular emphasis on the role of proteins in this process. Rating: 9 out of 10.
Article
Biochemistry & Molecular Biology
Mateusz Banach
Summary: This paper presents an update to the ellipsoid profile algorithm (EP) which measures the globularity of protein structures without calculating molecular surfaces. The algorithm compares the volume of the voxelized representation of the atoms with the volume of voxels that can fit inside an enclosing ellipsoid. The updated EP algorithm includes an improved outlier detection subroutine based on principal component analysis, which enhances its performance in distinguishing between dense and disordered regions of molecules.
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Leszek Konieczny
Summary: The structural transformation producing amyloids provides new insights into the protein folding problem. Analysis of the polymorphic structures of a-synuclein amyloid reveals a dominant distribution consistent with the micelle-like system. This ordering of hydrophobicity distribution covers a spectrum from micelle-like forms to structures with different patterns, all influenced by the water environment and the common tendency of certain fragments of a-synuclein to accept micelle-like structuralization.
