Article
Chemistry, Multidisciplinary
Vasilii S. Kolmogorov, Alexander S. Erofeev, Emily Woodcock, Yuri M. Efremov, Aleksei P. Iakovlev, Nikita A. Savin, Anna V. Alova, Svetlana V. Lavrushkina, Igor I. Kireev, Alexandra O. Prelovskaya, Elena V. Sviderskaya, Denis Scaini, Natalia L. Klyachko, Peter S. Timashev, Yasufumi Takahashi, Sergey V. Salikhov, Yuri N. Parkhomenko, Alexander G. Majouga, Christopher R. W. Edwards, Pavel Novak, Yuri E. Korchev, Petr V. Gorelkin
Summary: A high-resolution estimation method for mechanical properties and the possibility of qualitative and quantitative analysis of living cells have been demonstrated in this study. Forces applied using a nanopipette are much smaller than those using atomic force microscopy, with no detectable effect on live cells.
Article
Chemistry, Physical
Zhuoling Jiang, Kah-Meng Yam, Na Guo, Lishu Zhang, Lei Shen, Chun Zhang
Summary: By using the newly proposed steady-state DFT method, it was discovered that there exists a novel non-equilibrium effect in silane junctions, which can quickly drive thiol-terminated silanes from equilibrium to non-equilibrium states, overturning the previous standard DFT method.
NANOSCALE HORIZONS
(2021)
Article
Chemistry, Multidisciplinary
Juan D. Olarte-Plata, Jordan Gabriel, Pablo Albella, Fernando Bresme
Summary: The study focuses on utilizing Janus nanoparticles with different compositions to control temperature field distribution and achieve anisotropic heating at the nanoscale. Through simulations and experiments, it is found that the contrasting interfacial thermal conductances of JNPs can lead to temperature difference between both sides of the nanoparticle, thereby affecting the interfacial fluid temperature.
Review
Physics, Applied
Gang Chen
Summary: Phonon heat conduction at the microscale and nanoscale exhibits complex phenomena beyond the traditional predictions of Fourier's law, attracting wide attention. The development in studying phonon heat conduction phenomena reveals that besides classical size effects, other novel phenomena have emerged, often occurring at microscale and nanoscale, or only at elevated temperatures.
NATURE REVIEWS PHYSICS
(2021)
Article
Thermodynamics
B. Davier, P. Dollfus, N. D. Le, S. Volz, J. Shiomi, J. Saint-Martin
Summary: The study introduces a simple and easy-to-handle semi-analytical model to describe heat transport in heterostructures of various lengths. By redefining certain intrinsic parameters, the model accurately predicts thermal conductance and temperature profiles in different phonon transport regimes.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2022)
Review
Mechanics
Nikita Kavokine, Roland R. Netz, Lyderic Bocquet
Summary: Nanofluidics has become a new field in fluid mechanics, exploring novel properties in fluids at the nanoscale; Recent advancements in fabrication technology have led to the design of artificial nanofluidic systems at the scale of biological nanopores, driving the development of new experimental techniques and theoretical tools; This review serves as a toolbox for studying fluids at the nanometer scale, presenting basic equations, breakdown of equations, and emergence of new properties in molecular-scale confinement.
ANNUAL REVIEW OF FLUID MECHANICS, VOL 53
(2021)
Article
Chemistry, Analytical
Yasufumi Takahashi, Yuya Sasaki, Takeshi Yoshida, Kota Honda, Yuanshu Zhou, Takafumi Miyamoto, Tomoko Motoo, Hiroki Higashi, Andrew Shevchuk, Yuri Korchev, Hiroki Ida, Rikinari Hanayama, Takeshi Fukuma
Summary: Scanning ion conductance microscopy (SICM) is a promising tool for visualizing the dynamics of nanoscale cell surface topography. However, the lack of guidelines for fabricating nanopipettes with ideal shape has hindered SICM imaging at the submicron scale. In this study, we developed a simple and reproducible method for fabricating nanopipettes with sub-20nm apertures and demonstrated improved spatial resolution for nanoscale time-lapse topographic imaging.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Nathan D. Bamberger, Dylan Dyer, Keshaba N. Parida, Tarek H. El-Assaad, Dawson Pursell, Dominic V. McGrath, Manuel Smeu, Oliver L. A. Monti
Summary: Structure-function relationships are important in investigating the fundamentals of molecular electronics. This study emphasizes the need for nuanced relationships even for simple structures, using stilbene derivatives as a case study. The presence of multiple structural factors can unexpectedly control quantum transport in these molecules.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Physical
Tingwei Gao, Chunhui He, Chenguang Liu, Yinqi Fan, Cezhou Zhao, Chun Zhao, Weitao Su, Yannick J. Dappe, Li Yang
Summary: The use of graphene as a new type of electrode at molecular junctions has led to enhanced conductance for longer molecules. Studies involving oligopthiophene based hybrid gold-graphene junctions show similar behavior to alkane-based junctions, as supported by experiments and DFT calculations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Polymer Science
J. K. Wenderott, Ban Xuan Dong, Jojo A. Amonoo, Peter F. Green
Summary: Key physical properties of polymer films at nanoscale thickness are influenced by the thickness-dependent behavior, mainly associated with intermolecular interactions between the film and external interfaces. Conflicting experimental observations regarding T-g trends and dynamics at the nanoscale have been addressed through direct quantitative measurements of interfacial interactions using Kelvin force probe microscopy. This provides pathways to reconcile the contradictions and has broader implications for understanding the physical properties of polymer films in the nanoscale thickness regime.
Article
Materials Science, Multidisciplinary
J. Z. Sun
Summary: The study reveals the room temperature current-voltage (IV) characteristics of CoFeB vertical bar MgO vertical bar CoFeB type perpendicularly magnetized tunnel junctions exhibit a nonlinear bias voltage dependence, indicative of inelastic spin-flip scattering in the electrodes. A phenomenological model is constructed linking parameters of inelastic events related to spin-flip scattering with magnetoresistance and spin-transfer torque, providing measurable electrode-specific properties such as interface exchange stiffness impacting spin-torque performance.
Article
Chemistry, Multidisciplinary
Magatte N. Gueye, Alexandre Vercouter, Remy Jouclas, David Guerin, Vincent Lemaur, Guillaume Schweicher, Stephane Lenfant, Aleandro Antidormi, Yves Geerts, Claudio Melis, Jerome Cornil, Dominique Vuillaume
Summary: The study found significant differences in the nanoscale thermal conductivity of BTBT and C8-BTBT-C8 films, with BTBT showing higher values than C8-BTBT-C8. Molecular dynamics calculations supported this, showing significant thermal conductivity values along the crystal directions with anisotropy factors below 1.8 for BTBT and below 2.8 for C8-BTBT-C8.
Article
Chemistry, Multidisciplinary
Anni Feng, Songjun Hou, Juanzhu Yan, Qingqing Wu, Yongxiang Tang, Yang Yang, Jia Shi, Zong-Yuan Xiao, Colin J. Lambert, Nanfeng Zheng, Wenjing Hong
Summary: Quantum-tunneling-based nanoelectronics has the potential to miniaturize electronics to below 5 nm. This study investigates the conductance of well-defined silver nanoclusters with varying sizes. The results show that the conductance increases with cluster size, contrary to the behavior of organic molecules. The study suggests that these nanoclusters can be used as building blocks for nanodevices in the sub-5 nm size range.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Pan Li, Sven H. C. Askes, Esther del Pino Rosendo, Freek Ariese, Charusheela Ramanan, Elizabeth von Hauff, Andrea Baldi
Summary: In this work, temperature measurements at the nanoscale were achieved by exploiting the combination of surface-enhanced Raman spectroscopy and the temperature dependence of Raman peaks in beta-CuPc. The temperature of plasmonic gold nanoparticles under laser irradiation was determined by measuring the temperature-dependent Raman shifts of beta-CuPc films coated on an array of Au nanodisks and using calibration curves. The extracted temperatures were confirmed to be consistent with numerical modeling results.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Multidisciplinary
Dudong Feng, Xiaolong Yang, Xiulin Ruan
Summary: We demonstrate the potential of engineering phonon scattering, such as through isotope enrichment and temperature modulation, in achieving unconventional radiative heat transfer at the nanoscale between two boron arsenide bulks. This has promising applications in nonlinear thermal circuit components. Our work proposes a heat flux regulator and other nonlinear thermal radiative devices, benefiting from the design space enabled by isotope and temperature engineering of the phonon linewidth. Our findings highlight the capability of temperature and isotope engineering in designing and optimizing nonlinear radiative thermal devices and demonstrate the potential of phonon engineering in thermal radiative transport.
Article
Chemistry, Physical
Leopoldo Mejia, Ulrich Kleinekathoefer, Ignacio Franco
Summary: Under resonant transport conditions, the accuracy of the Landauer approximation depends on intramolecular interactions, while under nonresonant conditions, the emergence of transport routes beyond Landauer is determined by charging and discharging processes at the electrode-molecule interface. In both cases, decreasing the rate of charge exchange between the electrodes and molecule and increasing the interaction strength with the thermal environment result in decreased accuracy of Landauer.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Vinaya Kumar Golla, Claudio Piselli, Ulrich Kleinekathoefer, Roland Benz
Summary: This study investigates the permeation of fosfomycin through OprP and OprO channels in Pseudomonas aeruginosa bacteria using electrophysiology and molecular dynamics simulations. The results show that fosfomycin has higher binding affinity to OprP and OprO compared to fosmidomycin, and that arginine residues and lysine residue clusters play an important role in fosfomycin permeation. This study provides molecular insights on improving antibiotic permeation into Gram-negative bacteria, particularly resistant P. aeruginosa strains.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Tanzir Ahmed, Jayesh Arun Bafna, Roland Hemmler, Karsten Gall, Richard Wagner, Mathias Winterhalter, Michael J. Vellekoop, Sander van den Driesche
Summary: This work presents a microsystem setup for sensitive biological membrane translocation measurements. Thin free-standing synthetic bilayer lipid membranes (BLM) are constructed in microfabricated silicon nitride apertures and used for electrophysiological measurements of pore proteins. The integration of pore-forming proteins is achieved through direct reconstitution or reconstitution via outer membrane vesicles (OMVs) released from Gram-negative bacteria. This microsystem allows for investigation of fast gating events, pore blocking, and gating events of small pores.
Article
Chemistry, Multidisciplinary
Jiajun Wang, Jigneshkumar Dahyabhai Prajapati, Fan Gao, Yi-Lun Ying, Ulrich Kleinekathoefer, Mathias Winterhalter, Yi-Tao Long
Summary: Chirality is important but often overlooked in biological and chemical processes due to technical limitations. Researchers have used an electrostatically asymmetric membrane channel to successfully identify chiral amino acids in single peptides. This study provides a new approach for developing chiral recognition and protein sequencing methods.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Plant Sciences
Sayan Maity, Ulrich Kleinekathoefer
Summary: This mini review focuses on recent advances in the atomistic modeling of biological light-harvesting (LH) complexes. Multiscale methods are required to investigate the dynamical and spectroscopic properties of LH complexes due to their size and sophisticated electronic structures. The recently developed multiscale approach based on the density functional tight-binding framework has shown superior performance in describing the internal vibrational dynamics of pigment molecules and yields spectral densities in good agreement with experimental data.
PHOTOSYNTHESIS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Claudio Piselli, Vinaya Kumar Golla, Roland Benz, Ulrich Kleinekathoefer
Summary: This study focuses on the characterization of the lysine cluster in OprO, a porin protein in the outer membrane of Pseudomonas aeruginosa. The importance of lysine residues in ion conductance and phosphate ion flow was demonstrated through experiments and simulations. The results suggest that an improved understanding of lysine residues and ion mobility could lead to the development of more effective antibiotics for P. aeruginosa.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2023)
Article
Biochemistry & Molecular Biology
Igor V. Bodrenko, Tsedenia Alemu Zewdie, Jiajun Wang, Eshita Paul, Susanne Witt, Mathias Winterhalter
Summary: This study investigates protein-protein interaction using electrophysiology, focusing on the structure of the TolC-AcrA-AcrB complex and the inhibitory effect of potential efflux pump inhibitors. The findings suggest that the fluctuation of ion current and the average current through the TolC channel can be used as complementary measures to assess the interaction of the complex.
Article
Chemistry, Medicinal
Abhishek Acharya, Ishan Ghai, Claudio Piselli, Jigneshkumar Dahyabhai Prajapati, Roland Benz, Mathias Winterhalter, Ulrich Kleinekathoefer
Summary: In this study, the molecular mechanism of an antibiotic permeating through a bacterial channel is revealed, with a focus on the role of conformational dynamics of the constriction loop. The dynamics of the L3 loop, specifically the F118 to S125 segment, at the constriction regions of the OmpF porin is investigated using temperature accelerated sliced sampling approach. The importance of hydrogen-bond stabilization in the conformational dynamics of the L3 loop is demonstrated through single channel electrophysiology experiments and applied-field simulations. The findings suggest that conformational dynamics of the constriction loop may play a general role in antibiotic permeation through porins.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biophysics
Abhishek Acharya, Kalyanashis Jana, Dominik Gurvic, Ulrich Zachariae, Ulrich Kleinekathofer
Summary: Predicting molecular permeability and evaluating the effect of molecular transformations on permeation rates are critical for the development of effective antibiotics. In this study, a computational approach using Brownian dynamics is proposed to obtain estimates of molecular permeability through a porin channel within hours. The method is significantly faster compared with previous approaches and shows good correlation with experimental results. The potential applications of this method in high-throughput screening for fast permeators are discussed.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Yao Chen, Andrea Barba-Bon, Bohumir Gruner, Mathias Winterhalter, M. Alphan Aksoyoglu, Sushil Pangeni, Maryam Ashjari, Klaudia Brix, Giulia Salluce, Yeray Folgar-Camean, Javier Montenegro, Werner M. Nau
Summary: Cobalt bisdicarbollides (COSANs) are used as selective and efficient molecular carriers to transport hydrophilic oligopeptides through membranes. They can permeate lipid bilayer membranes without causing membrane damage. COSANs transport arginine-rich and lysine-rich peptides effectively, but cannot transport small molecules or anionic cargos. The transportation mechanism is a molecular carrier mechanism, and living cell experiments show that a fluorescent peptide cargo can be delivered into the cytosol.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Yannick Holtkamp, Markus Kowalewski, Jens Jasche, Ulrich Kleinekathofer
Summary: The theory of open quantum systems is important for understanding various processes in nature. Machine learning techniques have been developed to reduce computational effort in accurately describing dissipative quantum dynamics. However, previous methods require expensive training datasets, limiting their use for larger systems. In this study, a new machine-learned correction term is introduced, trained on data from numerically feasible small systems. It outperforms a previously handcrafted correction and improves the determination of dissipative quantum dynamics for larger systems.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Vivin Vinod, Sayan Maity, Peter Zaspel, Ulrich Kleinekathoefer
Summary: Accurate and fast calculation of molecular excited states remains a challenging topic. This study proposes a multifidelity machine learning approach that combines a small amount of highly accurate training data with cheaper and less accurate data to achieve high accuracy. The approach is applied to predict vertical excitation energies for three molecules, benzene, naphthalene, and anthracene, and achieves comparable accuracy to a machine learning model built solely on high-cost training data.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Jan P. Goetze, Sayan Maity, Ulrich Kleinekathoefer
Summary: This study investigates the FRET between the FMO protein complex and the CBP using an idealized model. It is found that the FRET efficiency is independent of the FMO trimer orientation, indicating that FMO acts as a robust spatial funnel for CBP excitation harvesting.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Multidisciplinary Sciences
Javier Abellon-Ruiz, Kalyanashis Jana, Augustinas Silale, Andrew M. Frey, Arnaud Basle, Matthias Trost, Ulrich Kleinekathoefer, Bert van den Berg
Summary: The uptake of vitamin B-12 is important for the colonization of the gut by Bacteroides species. In this study, the authors investigate the B-12 uptake in Bacteroides thetaiotaomicron, showing that it is mediated by stable outer membrane protein complexes consisting of surface-exposed BtuG lipoproteins and BtuB TonB-dependent transporters.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Stefan Milenkovic, Jiajun Wang, Silvia Acosta-Gutierrez, Mathias Winterhalter, Matteo Ceccarelli, Igor V. Bodrenko
Summary: Transmembrane beta-barrel proteins are versatile candidates for various technological applications and their behavior is influenced by environmental conditions. Comparing two highly homologous porins, OmpF and OmpC, we observed subtle amino acid substitutions that can modulate mass transport properties. These differences can be attributed to the disparities in the environmental conditions under which the porins are expressed. Our analysis not only highlights the advantages of enhanced sampling methods, but also provides valuable insights into the biological function and technical applications of these proteins.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
