Article
Chemistry, Multidisciplinary
Shuji Fujisawa, Kazuho Daicho, Ayhan Yurtsever, Takeshi Fukuma, Tsuguyuki Saito
Summary: All-atom molecular dynamics simulations and atomic force microscopy were used to study the structural dynamics of single nanocellulose during drying. It was discovered that the twist morphology of nanocellulose becomes localized along the fibril axis in the final stage of drying. Conformational changes at C6 hydroxymethyl groups and glycoside bond were also observed, indicating an increase in crystallinity during the drying process. These insights provide valuable information for understanding the nanocellulose structures in material processing and designing materials with advanced functionalities.
Article
Chemistry, Physical
Maria J. Rodriguez-Espinosa, Javier M. Rodriguez, Jose R. Caston, Pedro J. de Pablo
Summary: In this study, we investigated the cargo retention of individual human picobirnavirus virus-like particles with different N-terminal topologies of the capsid protein. Our results show that these different topologies result in distinct cargo release dynamics during mechanical disassembly experiments due to their different interaction with RNA.
NANOSCALE HORIZONS
(2023)
Article
Chemistry, Multidisciplinary
Shun Sasano, Ryo Ishikawa, Gabriel Sanchez-Santolino, Hiromichi Ohta, Naoya Shibata, Yuichi Ikuhara
Summary: Lithium lanthanum titanate (LLTO) is a promising candidate for electrolytes in all-solid-state Li-ion batteries due to its high Li-ion conductivity, but the Li-ion conductivity at grain boundaries is significantly reduced. This reduction is caused by the formation of oxygen vacancies and subsequent positive charge at the grain boundary, creating Li-ion depletion layers that greatly reduce Li-ion conductivity.
Article
Polymer Science
Gregory Meyers, Rajesh Paradkar, Ester Caro, Wenzhao Yang, Kenneth Kearns
Summary: This article describes various atomic force microscopy methods for imaging and measuring the modulus of polyethylene layers in a five-layer multilayer film. The methods can distinguish the layers based on different signals and are highly sensitive to density differences, with statistically significant results.
Article
Chemistry, Multidisciplinary
Haruhiko Eki, Katsuhiko Abe, Hiroshi Sugiyama, Masayuki Endo
Summary: This study used atomic force microscopy to directly observe the formation and degradation of tensegrity triangle DNA crystals at a molecular level, visualizing the dynamic process and characterizing them with nanoscale resolution.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Marcel Hanke, Niklas Hansen, Emilia Tomm, Guido Grundmeier, Adrian Keller
Summary: The study investigated the denaturation of DNA origami nanostructures by different Gdm salts, with guanidinium thiocyanate being the most potent denaturant. The results also revealed a non-monotonous temperature dependence of DNA origami denaturation in guanidinium sulfate, emphasizing the complexity of Gdm-DNA interaction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Toshiaki Nakano, Ken Akamatsu, Masataka Tsuda, Ayane Tujimoto, Ryoichi Hirayama, Takeshi Hiromoto, Taro Tamada, Hiroshi Ide, Naoya Shikazono
Summary: This study established a method to evaluate the yield and complexity of clustered DNA damage in irradiated cells using atomic force microscopy. It was found that clustered DNA damage is a signature of ionizing radiation, and Fe ion beams produce clustered DNA damage with high complexity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Nanoscience & Nanotechnology
Keivan Asadi, Junghoon Yeom, Hanna Cho
Summary: Investigating internal resonance (IR) mechanisms in micro/nanoresonators reveals that intermodal coupling between second and third flexural modes in asymmetric structures provides an optimal condition for strong IR, with high energy transfer to the resonated mode. This study introduces design strategies that can be easily integrated into typical micro/nanoelectromechanical systems, offering potential for paradigm-shifting applications in micro/nanosystems.
MICROSYSTEMS & NANOENGINEERING
(2021)
Editorial Material
Multidisciplinary Sciences
Telmo O. Paiva, Albertus Viljoen, Yves F. Dufrene
Summary: Advancements in atomic force microscopy (AFM) techniques and methodologies in microbiology have enhanced our understanding of microbial cell surfaces. Recent studies have shown that AFM imaging of cells and membranes at or near molecular resolution enables detailed visualization of membrane-drug interactions.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Alex Evilevitch, Sophia Hohlbauch
Summary: This study investigated the mechanical response of the nucleus during the initial stage of herpesvirus infection by using atomic force microscopy. It was found that the chromatin becomes stiffer while the nuclear lamina becomes softer after the injection of viral DNA, which may contribute to maintaining nuclear integrity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Polymer Science
Mengxi Zheng, Qian Li, Victoria E. Paluzzi, Jong Hyun Choi, Chengde Mao
Summary: Supramolecular polymers have unique characteristics, DNA is used as a model system to engineer innovative, nanoscaled morphologies of supramolecular polymers, obtaining a range of polymer morphologies including straight chains, spirals, and closed rings with finite sizes.
MACROMOLECULAR RAPID COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Javier Sotres, Hannah Boyd, Juan F. Gonzalez-Martinez
Summary: Scanning probe microscopies offer a powerful tool for investigating surfaces at the nanoscale, but their full potential is hindered by the need for experienced users, data analysis challenges, and time-consuming experiments. Researchers have developed an algorithm utilizing deep learning techniques to control the operation of an Atomic Force Microscope (AFM), bringing SPM closer to full autonomous operation.
Article
Physics, Applied
Shiquan Lin, Zhong Lin Wang
Summary: Inspired by TENG, scanning TENG is proposed for local surface charge density measurement using atomic force microscopy. The technique taps a conductive tip above a charged dielectric surface to induce an AC, with Fourier analysis showing a linear relation to surface charge density. Results demonstrate its power in probing nanoscale charge transfer in contact-electrification.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Physical
Patrick Lemoine, Chris Dooley, Alessio Morelli, Emma Harrison, Dorian Dixon
Summary: Gold nanoparticles functionalized with PEG and peptide ligands were examined using atomic force microscopy (AFM) to study their morphology and properties. The results showed that PEG and peptide ligands have similar affinity to the gold surface, but exhibit differences in morphology, cohesion, and hydrophilicity at the nanolevel.
APPLIED SURFACE SCIENCE
(2022)
Article
Chemistry, Physical
Yeyue Xiong, Saeed Izadi, Alexey Onufriev
Summary: The article introduces a globally optimal polarizable water model, OPC3-pol, which accurately simulates water molecules at the atomic scale with minimal computational overheads. The model demonstrates improved computational efficiency and structure stability compared to existing approaches.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemical Research Methods
Benjamin Martin, Pablo D. Dans, Milosz Wieczor, Nuria Villegas, Isabelle Brun-Heath, Federica Battistini, Montserrat Terrazas, Modesto Orozco
Summary: The study explores the role of organic ions in the stability of DNA duplexes and its implications for self-replication of nucleic acids. The researchers found that the presence of certain amino acids in the primordial soup, such as Arginine and Lysine, can stabilize DNA duplexes and reduce the stability difference between AT- and GC-rich duplexes. This suggests that organic ions, which have been largely ignored in the study of DNA, could have played a crucial role in the early replication of DNA before the existence of enzymatic machinery.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Review
Biophysics
Gabriela da Rosa, Leandro Grille, Victoria Calzada, Katya Ahmad, Juan Pablo Arcon, Federica Battistini, Genis Bayarri, Thomas Bishop, Paolo Carloni, Thomas Cheatham Iii, Rosana Collepardo-Guevara, Jacek Czub, Jorge R. Espinosa, Rodrigo Galindo-Murillo, Sarah A. Harris, Adam Hospital, Charles Laughton, John H. Maddocks, Agnes Noy, Modesto Orozco, Marco Pasi, Alberto Perez, Daiva Petkeviciute-Gerlach, Rahul Sharma, Ran Sun, Pablo D. Dans
Summary: The structure and dynamical properties of B-DNA have long been a central topic in biology, chemistry, and physics, with its flexibility and structural polymorphism affecting its functionality and regulation. Understanding the sequence-dependent structural properties of B-DNA helps to rationalize its interactions with ligands and proteins, revealing the structural basis of gene regulation.
BIOPHYSICAL REVIEWS
(2021)
Article
Biochemical Research Methods
Genis Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluis Gelpi
Summary: The BioBB REST API extends and complements the BioBB library, offering programmatic access to the collection of biomolecular simulation tools included in the BioExcel Building Blocks library.
Article
Biochemistry & Molecular Biology
Genis Bayarri, Pau Andrio, Modesto Orozco, Josep Lluis Gelpi
Summary: BioExcel Building Blocks Workflows is a web-based graphical user interface that provides access to a collection of pre-configured biomolecular simulation workflows. It offers a high level of interactivity and integrates multiple tools and features to streamline common processes in biomolecular simulation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Marti Checa, Xin Jin, Ruben Millan-Solsona, Sabine M. Neumayer, Michael A. Susner, Michael A. McGuire, Andrew O'Hara, Gabriel Gomila, Petro Maksymovych, Sokrates T. Pantelides, Liam Collins
Summary: This study uses quantitative scanning probe microscopy methods combined with density functional theory to explore the nanoscale variability in the dynamic functional properties of the ferroelectric material CIPS and the nonferroelectric material IPS. It reveals evidence of fast ionic transport that mediates a significant out-of-plane electromechanical response of the CIPS surface in the paraelectric phase. It also recovers the local dielectric behavior during the ferroelectric-paraelectric phase transition and demonstrates the tunable conductivity enhancement at the CIPS/IPS interface.
Article
Biochemistry & Molecular Biology
Maria Victoria Neguembor, Juan Pablo Arcon, Diana Buitrago, Rafael Lema, Jurgen Walther, Ximena Garate, Laura Martin, Pablo Romero, Jumana AlHaj Abed, Marta Gut, Julie Blanc, Melike Lakadamyali, Chao-ting Wu, Isabelle Brun Heath, Modesto Orozco, Pablo D. Dans, Maria Pia Cosma
Summary: The linear sequence of DNA provides important information about genes and their regulatory elements, but understanding gene function and regulation also requires knowledge of how genes fold in three-dimensional nuclear space. This study introduces immuno-OligoSTORM, an imaging strategy that allows super-resolution visualization of nucleosomes within specific genes by simultaneous visualization of DNA and histones. By combining immuno-OligoSTORM with modeling approaches, the method called Modeling immuno-OligoSTORM enables quantitative modeling of genes at nucleosome resolution and provides information about chromatin accessibility for regulatory factors.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Physical
Mirko Paulikat, Juan Aranda, Emiliano Ippoliti, Modesto Orozco, Paolo Carloni
Summary: The authors used classical molecular dynamics and quantum mechanics/molecular mechanics methods to investigate proton transfer processes in N-ESI/IM-MS, and validated the simulation results with experimental data. The study revealed that the distribution of protons depends on the hydration level of the analytes and the size of droplets formed during electrospray experiments.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Aakash Basu, Dmitriy G. Bobrovnikov, Basilio Cieza, Juan Pablo Arcon, Zan Qureshi, Modesto Orozco, Taekjip Ha
Summary: In this study, we comprehensively characterized the mechanical code of DNA using high-throughput experimental methods and developed a physical model to describe the sequence and methylation dependence of DNA deformation. Our measurements and model validations demonstrated that sequence and epigenetic modifications can encode regulatory information in diverse contexts.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Larissa Huetter, Adrica Kyndiah, Gabriel Gomila
Summary: This work presents the analytical physical modeling of undoped organic metal-electrolyte-semiconductor (OMES) capacitors, and analyzes the dependence of physical device parameters. The study shows that ionic diffusive effects in the electrolyte can significantly affect the device response.
ADVANCED THEORY AND SIMULATIONS
(2023)
Article
Chemistry, Multidisciplinary
Israel Serrano-Chacon, Bartomeu Mir, Lorenzo Cupellini, Francesco Colizzi, Modesto Orozco, Nuria Escaja, Carlos Gonzalez
Summary: We studied a DNA oligonucleotide that forms two different i-motif structures depending on pH and temperature. At neutral pH, the major structure is stabilized by C:C+ base pairs and G:C:G:C tetrads. At pH 5, a more elongated i-motif structure with C:C+ base pairs and G:T:G:T tetrads is observed. Molecular dynamics calculations showed that the conformational transition between the two structures is driven by the protonation state of key cytosines. This study reveals the pH-dependent plasticity and conformational switch of i-motif structures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Larissa Huetter, Adrica Kyndiah, Gabriel Gomila
Summary: This article presents the analytical physical modeling of undoped electrolyte gated organic field effect transistors (EGOFETs) in the Helmholtz approximation. A compact analytical model for the current-voltage (I-V) characteristics, including the effects of access series resistance, has been derived and validated by 2D finite element numerical calculations. The model describes all operating regimes continuously, covers small channel lengths, and only includes physical device parameters. Analytical expressions for phenomenological parameters in the ideal FET model have been proposed. The derived analytical physical model provides a simple and quantitative way to analyze the electrical characteristics of EGOFETs beyond the oversimplified ideal FET model.
ADVANCED THEORY AND SIMULATIONS
(2023)
Article
Chemistry, Medicinal
Federica Battistini, Alba Sala, Adam Hospital, Modesto Orozco
Summary: The properties of DNA duplex have been accurately described using molecular dynamics simulations, but there lacks equivalent simulations for RNA duplex which is usually represented as a rigid rod. In this study, a massive simulation effort was conducted to derive the properties of RNA duplex and a simplified model for long RNA duplexes. Despite high chemical similarity, the local and global elastic properties of DNA and RNA duplexes are significantly different. Statement about the relative flexibility or stability of both polymers is meaningless and a detailed description depending on the sequence and deformation type should be used.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Leandro Grille, Diego Gallego, Leonardo Darre, Gabriela da Rosa, Federica Battistini, Modesto Orozco, Pablo D. Dans
Summary: The characterization of RNA backbone conformations is complex, and accurate measurement of pseudotorsional angles is crucial. Combining data from different sources provides a comprehensive representation of RNA accessible space. Protein interactions play a significant role in influencing the population of RNA backbone conformations.
Article
Chemistry, Multidisciplinary
Israel Serrano-Chacon, Bartomeu Mir, Lorenzo Cupellini, Francesco Colizzi, Modesto Orozco, Nu'ria Escaja, Carlos Gonzalez
Summary: We studied a DNA oligonucleotide that can form two different i-motif structures, with their stability depending on pH and temperature. The structure at neutral pH is stabilized by C:C+ base pairs and G:C:G:C tetrads. At pH 5, a more elongated structure consisting of C:C+ base pairs and G:T:G:T tetrads is observed. The transition between these two structures is driven by the protonation state of key cytosines.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Juan Aranda, Milosz Wieczor, Montserrat Terrazas, Isabelle Brun-Heath, Modesto Orozco
Summary: We used molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to elucidate the replication mechanism of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Our findings showed that the viral RdRp is highly processive and has a higher catalytic rate of incorporation compared to human RNA Pol II. Furthermore, we observed that remdesivir, an antiviral nucleotide, is incorporated more slowly into the RNA than ATP, suggesting it is not a competitive inhibitor. Overall, this study provides a detailed understanding of the replication mechanism of RdRp.