Article
Chemistry, Physical
Hai Xu, Henghao Yu, Yingjie Chen, Jing Deng, Zhaoyu Chen, Peng Zhou, Jian R. Lu, Jun Yang, Yurong Zhao
Summary: Zippers between complementary sidechains have potential in preparing peptide self-assemblies with long-range ordering. This study achieved well-defined nanostructures through nonpolar zippers by designing a series of short amphiphilic peptides. Only one peptide, Ac-I3VGK-NH2, could self-assemble into wide and uniform nanoribbons, thanks to the formation of extensive nonpolar zippers between beta-sheets. The failure of other peptide variants highlighted the importance of the interaction mode of hydrophobic sidechains in the formation of wide and flat nanoribbons.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2023)
Article
Chemistry, Physical
Li Deng, Yanting Wang
Summary: A multi-scale computational approach has been introduced to predict the beta-sheet morphology self-assembled by short peptides in aqueous solution based on the molecular structure of the peptide. The computational results confirm that peptides with higher inter-sheet interaction tend to form tube-like structures with larger width, while peptides with lower ratios tend to form fibril structures with smaller width, which is consistent with experimental observations.
MOLECULAR SIMULATION
(2021)
Article
Chemistry, Physical
Yu Zhu, Abash Sharma, Eric J. Spangler, Mohamed Laradji
Summary: The adhesion modes of spherical Janus nanoparticles on planar membranes were investigated through molecular dynamics simulations. It was found that the nanoparticles exhibited rich phase behavior depending on their adhesion energy density and areal number density. At intermediate densities and intermediate to high adhesion energy density, repulsive membrane-curvature-mediated interactions caused the nanoparticles to self-assemble into an ordered hexagonal superlattice.
Article
Electrochemistry
Ilya I. Ryzhkov, Margarita A. Shchurkina, Elena Mikhlina, Mikhail M. Simunin, Ivan Nemtsev
Summary: Nanoporous membranes with electrically conductive surface are an important class of stimuli-responsive materials. The variation of surface potential allows for adjusting ionic selectivity, conductivity, and rejection. This work focuses on the theoretical and experimental study of switchable ionic selectivity, providing insights into ion transport in stimuli-responsive membranes operated by electric field.
ELECTROCHIMICA ACTA
(2021)
Article
Engineering, Chemical
Miao Deng, Zhen Lin, Chuan Hu, Qiugen Zhang
Summary: This study demonstrates a novel approach using interfacial polymerization (IP) to fabricate polyamide (PA) nanofiltration membranes (NFMs) with fast desalination performance. By forming sacrificial interlayers of copper hydroxide nanostrands (CuNS) and sodium polystyrene sulfonate (PSS) on polyvinylidene fluoride (PVDF) substrates, abundant piperazine (PIP) monomers can be stored and their distribution can be regulated through charge-driven assembly, resulting in the formation of defect-free PA layers on large-porous substrates.
JOURNAL OF MEMBRANE SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Lanlan Yu, Zhun Deng, Wenbo Zhang, Shuli Liu, Feiyi Zhang, Jianjian Zhou, Chunhua Ma, Chenxuan Wang
Summary: The study investigates the effects of two immobilized cations (ammonium and guanidinium) on the structure of melittin, showing that the differences in lysine and arginine side chains lead to opposite folding and assembly effects.
FRONTIERS IN CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Torsten John, Stefania Piantavigna, Tiara J. A. Dealey, Bernd Abel, Herre Jelger Risselada, Lisandra L. L. Martin
Summary: This study investigates the impact of membrane models on peptide self-assembly and proposes a model for predicting the effects of cellular changes on peptide assembly. The presence of oxidative lipids has similar effects on peptide self-assembly as bacterial membrane mimetics. Peptides with different properties exhibit different responses to lipid environments, with electrostatic interactions playing a primary role.
Article
Biochemistry & Molecular Biology
Ekaterina Skolotneva, Kseniia Tsygurina, Semyon Mareev, Ekaterina Melnikova, Natalia Pismenskaya, Victor Nikonenko
Summary: This study develops a mathematical model to investigate the diffusion process of ammonium ions in an anion-exchange membrane, considering the proton-exchange reactions between ammonium, water, and ammonia. The results show that the increase in pH in the membrane internal solution due to Donnan exclusion of H+ ions leads to a change in the principal nitrogen-atom carrier from NH4+ cation to NH3 molecule.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Engineering, Chemical
Qisong Xu, Jie Gao, Fan Feng, Tai-Shung Chung, Jianwen Jiang
Summary: Organic solvent nanofiltration (OSN) membranes are developed using a combination of machine learning, molecular simulation, and experiment. Machine learning models are constructed to identify critical properties and establish a relationship for permeability prediction. Molecular simulation provides microscopic insights, while experiments validate the predictions. This holistic approach advances the development of new membranes for solvent recovery and other separation processes.
JOURNAL OF MEMBRANE SCIENCE
(2023)
Article
Thermodynamics
Ziyuan Li, Yapeng Wang
Summary: With the increasing awareness of explosion protection due to the global terrorist threat, especially in recent years, explosion protection has become a worldwide issue. People are focusing more on the explosion-proof capabilities of buildings, particularly glass windows. Experimental methods are crucial for evaluating the explosion-proof performance of glass windows, providing valuable data for designing anti-explosion measures.
CASE STUDIES IN THERMAL ENGINEERING
(2021)
Article
Engineering, Environmental
Qichao Sun, Ye Zhou, Lianying Wu, Yangdong Hu, Weitao Zhang
Summary: This paper discusses the separation of five azeotropic systems with different molecular weights through simulation and experiment. A stable PDMS/PVDF-PTFE membrane with favorable mechanical properties was prepared, and the dissolution and diffusion processes of the azeotropic systems were simulated. The separation performance of the membrane was investigated and validated through experimental results, demonstrating the accuracy of the simulation.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Biophysics
Ye Li, Man Zhang, Xinhui Niu, Tongtao Yue
Summary: Clathrin-mediated endocytosis has selectivity for nanoparticle size, and clathrin can modulate the process and tune the selectivity. However, the size range of clathrin assembly does not match larger nanoparticles, and clathrin can also increase the barrier of membrane wrapping on larger nanoparticles by rigidifying the local membrane patch. The competition of these factors determines whether membrane wrapping on nanoparticles is promoted or suppressed, and can be adjusted by nanoparticle-membrane adhesion strength, clathrin concentration, and inter-nanoparticle distance.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Chemistry, Analytical
Dmitry Dyubo, Oleg Yu Tsybin
Summary: The ionized states of molecular analytes on solid surfaces and their effects on output generation in a dynamic PIN diode were investigated using computer simulations. The study identified new possibilities for implementing a nanobiosensor design based on a dynamic PIN diode with surface charge control.
Article
Chemistry, Physical
Lu Hou, Junfeng Wang, Sijia Wang, Wen-Cui Li, Guohui Li, An-Hui Lu
Summary: This study successfully synthesized asymmetric polymer nanocrescents and their carbonaceous analogues through a crystallization-assisted asymmetric assembly method. Molecular dynamics simulation revealed that the crescent structure is caused by the asymmetry distribution of octadecanol crystal within the hydrophobic core of triblock copolymer F127 micelles, where intermediate elliptic micelles with hydrophobic ends fuse with each other end-to-end at an angle to form curing nanocrescent morphology. This research will provide a valuable contribution to theoretical and technological researches.
Article
Engineering, Chemical
Niping Ma, Ke Xu, Jianhua Guo, Ning Wei, Junxia Yan
Summary: Molecular dynamics simulations were used to explore the sizes and distributions of nanopore/channels in graphene oxide (GO) membranes and the relationship between GO flakes size and membrane thickness. It was found that the size of GO flakes affects the distribution of nanopore sizes in GO membranes, but does not significantly impact the total nanopore area in membranes with the same thickness. The study also confirmed that the total nanopore area of GO membranes decreases exponentially as the membrane thickness increases. A columnar-array substrate model was developed to create customized GO membranes for specific filtration functions. These findings provide insights into the design of functional membranes for energy and environmental applications, and offer guidance for the practical application of GO membranes in separation and filtration.
Article
Biochemistry & Molecular Biology
Stephan L. Grage, Sergii Afonin, Marco Ieronimo, Marina Berditsch, Parvesh Wadhwani, Anne S. Ulrich
Summary: The lateral pressure profile, an important physical property of lipid bilayers, can be manipulated and probed using peptides residing in different regions of the membrane, according to this study.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Igor Komarov, Ganna Tolstanova, Halyna Kuznietsova, Natalia Dziubenko, Petro Yanchuk, Lydia Y. Shtanova, Stanislav P. Veselsky, Liudmyla Garmanchuk, Nataliia Khranovska, Oleksandr Gorbach, Taisa Dovbynchuk, Petro Borysko, Oleg Babii, Tim Schober, Anne S. Ulrich, Sergii Afonin
Summary: The study analyzed the efficacy of a photoswitchable cytotoxic peptide LMB040 on chemically induced hepatocellular carcinoma model in immunocompetent rats, finding that initial application of a less toxic form followed by in vivo photoconversion led to higher overall survival of the animals and enhanced immune response compared to untreated animals.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Beibei Meng, Stephan L. Grage, Oleg Babii, Masanari Takamiya, Neil MacKinnon, Tim Schober, Illia Hutskalov, Omar Nassar, Sergii Afonin, Serhii Koniev, Igor Komarov, Jan G. Korvink, Uwe Straehle, Anne S. Ulrich
Summary: A labeling strategy for in vivo F-19-MRI based on highly fluorinated, short hydrophilic peptide probes, is developed. These probes are functionalized further by a fluorophore and an alkyne moiety for bioconjugation. The design of the peptide probes ensures low cytotoxicity and high serum stability. The performance of these probes in F-19-MRI is demonstrated and they are found to exhibit high stability and long circulation times in living zebrafish embryos. Overall, these peptide probes are suitable for in vivo F-19-MRI applications.
Article
Biochemistry & Molecular Biology
Fabian Schweigardt, Erik Strandberg, Parvesh Wadhwani, Johannes Reichert, Jochen Buerck, Haroldo L. P. Cravo, Luisa Burger, Anne S. Ulrich
Summary: Amphipathic peptides exhibit antibiotic properties by permeabilizing cell membranes. KL peptides form amphipathic beta-strands in the presence of lipid bilayers and kill bacteria in a unique length-dependent manner. Experimental results demonstrate that KL peptides with 10-12 amino acids exhibit the best antimicrobial activity and low hemolytic side effects. The study suggests that the membrane disruption by KL peptides is achieved through a carpet mechanism.
Article
Chemistry, Multidisciplinary
Chun Li, Henrik Schopmans, Lukas Langer, Stefan Marschner, Abhinav Chandresh, Jochen Buerck, Youichi Tsuchiya, Adachi Chihaya, Wolfgang Wenzel, Stefan Braese, Mariana Kozlowska, Lars Heinke
Summary: Researchers have successfully prepared a crystalline film based on porphyrin with chiral properties and demonstrated excellent optoelectronic performance. By assembling in a metal-organic framework film, the porphyrin core becomes twisted and chiral. The close packing and crystalline order of the porphyrin cores in the film result in outstanding optoelectronic properties. Through exciting the Soret band of porphyrin, efficient photoconduction with a high On-Off ratio is achieved. Moreover, handedness-dependent circularly-polarized-light photoconduction is obtained. The combination of assembly-induced chirality with the rich porphyrin chemistry opens up possibilities for organic materials with exceptional chiral and optoelectronic properties.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Erik Strandberg, Parvesh Wadhwani, Jochen Buerck, Patrick Anders, Christian Mink, Jonas van den Berg, Raffaele A. M. Ciriello, Manuel. N. N. Melo, Miguel A. R. B. Castanho, Eduard Bardaji, Jakob. P. P. Ulmschneider, Anne. S. S. Ulrich
Summary: BP100 is a cationic undecamer peptide with antimicrobial and cell-penetrating activities. The configuration of this peptide in lipid bilayers depends on temperature and lipid composition. At high temperatures, BP100 lies flat on the membrane surface, while at lower temperatures near the lipid phase transition, the helix structure inserts into the membrane. This inserted state is stable in thin bilayers at low peptide concentrations, but higher peptide concentrations are required in thicker membranes.
Article
Chemistry, Multidisciplinary
Lisa Ross, Julius Reitemeier, Farhad Ghalami, Wen-Shan Zhang, Jurgen H. Gross, Frank Rominger, Sven M. Elbert, Rasmus Schroeder, Marcus Elstner, Michael Mastalerz
Summary: In this study, the solution and solid-state behavior of two-dimensionally triptycene end-capped QPPs were investigated. QPPs were synthesized through condensation reactions with pyrene-based tetraketone and ortho-diamines, resulting in the formation of dimers in solution, supported by MALDI-TIMS-TOF-MS analysis. Single-crystal X-ray analysis showed a short p-p distance of 3.3-3.4 angstrom and a perfect shape match during the dimerization of triptycene end-capped QPPs, indicating its potential as a synthon for crystal engineering.
CHINESE JOURNAL OF CHEMISTRY
(2023)
Review
Biophysics
T. Kubar, M. Elstner, Q. Cui
Summary: Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are essential for studying biomolecules. This article reviews the methodology of QM/MM approaches and their application to energy transduction in biomolecular machines. The importance of balancing efficiency and accuracy is emphasized, and examples showcase the value and limitations of QM/MM methodologies. Suggestions for further development in making QM/MM analyses more quantitative and applicable to complex biological problems are discussed.
ANNUAL REVIEW OF BIOPHYSICS
(2023)
Article
Chemistry, Physical
Denis Maag, Josua Boeser, Henryk A. Witek, Ben Hourahine, Marcus Elstner, Tomas Kubar
Summary: Coupled-perturbed equations for degenerate orbitals were implemented to study proton-coupled electron transfer reactions. The method was tested for both QM and QM/MM setups and showed stable enhanced sampling simulations. The obtained potentials of the mean force successfully described the thermodynamic and kinetic features of the reactions, making it a promising tool for investigating more complex systems like proteins.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Philipp M. Dohmen, Mila Kramer, Patrick Reiser, Pascal Friederich, Marcus Elstner, Weiwei Xie
Summary: In this study, the surface hopping method is used to simulate charge transport in organic semiconductors. Nonadiabatic molecular dynamics simulations are performed to study hole transport in anthracene and pentacene. Neural network based Hamiltonians are employed in two different nuclear relaxation schemes, and their performance in reproducing hole mobilities and inverse participation ratios is evaluated. The results show that the neural network models are able to accurately reproduce the desired properties with significantly reduced computational cost compared to traditional methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Ali Deniz Ozdemir, Samaneh Inanlou, Franz Symalla, Weiwei Xie, Wolfgang Wenzel, Marcus Elstner
Summary: This paper investigates the impact of structural disorder in amorphous organic semiconductors (OSCs) on the transfer parameters and charge mobilities. A sampling strategy for incorporating static and dynamic structural disorder is developed using QM/MM methods and extensive MD sampling. The results show that dynamic disorder causes an order of magnitude difference in the calculated mobility between morphologies of the same material. The method allows for the sampling of disorder in HOMO energies and couplings, and the statistical analysis characterizes the relevant time scales for charge transfer in these complex materials.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Frauke Greil, Rajalakshmi Punampalam, Torsten H. Walther, Stefan Heissler, Anne S. Ulrich
Summary: A novel solid phase of water stable at room temperature was believed to be accessible from hydrophilic surfaces by repeated perturbation of interfacial layers. However, a detailed biological and biochemical analysis revealed that the observed phenomena were likely due to accumulation of microbiological and organic contaminants, rather than a new solid phase of water. The same analysis also found that the presumed stable water aggregates in the lyophilized solid material consisted mainly of a conglomerate of bacteria, algae, and synthetic materials.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Hematology
Fabian Kutzki, Diego Butera, Angelina J. Lay, Denis Maag, Joyce Chiu, Heng-Giap Woon, Tomas Kubar, Marcus Elstner, Camilo Aponte-Santamaria, Philip J. Hogg, Frauke Graeter
Summary: This study revealed the oxidation state of disulfide bridges in the VWF-C4 domain and its implications for VWF's platelet binding function. It was found that two major force-bearing disulfide bonds are partially reduced in human blood, leading to conformational changes within C4 that affect the accessibility of the integrin-binding motif and impair integrin-mediated platelet binding. Additionally, specific thiol/disulfide exchanges between the reduced species and the remaining disulfide bridges were observed, with mechanical force potentially enhancing the proximity of reactant cysteines and further affecting integrin binding propensity.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2023)
Article
Materials Science, Multidisciplinary
Niklas J. Herrmann, Nadine von Coelln, Robin M. Teichgreber, Sebastian Hoefener, Christian Huck, Farhad Ghalami, Simon Settele, Manuel Hertzog, Marcus Elstner, Petra Tegeder, Eva M. Herzig, Jana Zaumseil
Summary: In this study, meniscus-guided zone-casting was used to selectively deposit two different polymorphs of PDIF-CN2 from solution. The two polymorphs can be distinguished by their characteristic low-wavenumber Raman modes and distinctive photoluminescence spectra, reflecting different intermolecular coupling. Despite having different crystalline structures, field-effect transistors based on thin films of both polymorphs show similar electron mobilities.
JOURNAL OF MATERIALS CHEMISTRY C
(2023)
Meeting Abstract
Biophysics
Parvesh Wadhwani, Saiguru Sekaran, Erik Strandberg, Jochen Burck, Archana Chugh, Anne S. Ulrich
BIOPHYSICAL JOURNAL
(2022)