Article
Chemistry, Multidisciplinary
Yang Wang, David W. Collinson, Heungdong Kwon, Robert D. Miller, Krystelle Lionti, Kenneth E. Goodson, Reinhold H. Dauskardt
Summary: Thermal transport in polymer nanocomposites is influenced by the interfacial thermal conductance, which is determined by the density of internal interfaces. However, there is a lack of experimental measurements linking thermal conductance to the chemistry and bonding between polymer molecules and the glass surface. To address this issue, polymers are confined in porous organosilicates with high interfacial densities. The thermal conductivities of the composites are measured using time-domain thermoreflectance, and the thermal boundary conductance is extracted using effective medium theory and finite element analysis. This analysis platform provides a new paradigm for studying heat flow across different domains.
Article
Chemistry, Physical
Duowei Lu, Pedram Fatehi
Summary: A mathematical model was developed to assess the interfacial interaction between rough spherical surfaces. The study found that the number and ratio of asperities were the primary parameters affecting the interfacial interaction. The arrangement and randomness in the position of asperities had negligible effects. Increasing the fractal dimension and relative fractal dimension enhanced the interfacial energy between surfaces, leading to increased stability of particles in suspension.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2022)
Article
Physics, Fluids & Plasmas
Thijs de Goede, Karla de Bruin, Noushine Shahidzadeh, Daniel Bonn
Summary: This paper investigates the influence of surface roughness on droplet splashing, showing that rough surfaces can change the splashing velocity of droplets. When the droplet roughness is large enough, it changes the droplet splashing mechanism from corona to prompt splashing. The study also demonstrates that the measured splashing velocity for water and ethanol on surfaces with different roughnesses can be collapsed onto a single curve, indicating that the droplet splashing velocity on rough surfaces scales with the Ohnesorge number defined with the surface roughness length scale.
PHYSICAL REVIEW FLUIDS
(2021)
Article
Chemistry, Physical
Euihyun Lee, Xiao You, Carlos R. Baiz
Summary: Studies have shown that the inverted-headgroup has no effect on the carbonyl H-bond populations or the interfacial water H-bond dynamics in lipids, but disrupts the H-bond structure of carbonyl-associated waters in the DOCPe bilayer, especially within the second hydration shell.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Man Wang, Yi Wan, Gongming Xin
Summary: In this study, the influence of vibration on the evaporation and boiling performance of water nanofilm on rough surfaces was investigated using molecular dynamics method. The results showed that vibration suppressed the atomization of water nanofilm, and the atomization modes varied with the amplitude and frequency of the vibration. For rough surfaces, the weakening of vibration-induced evaporation and boiling performance of water nanofilm was attributed to the reduction of surface hydrophilicity.
APPLIED SURFACE SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Manuel R. Uhlig, Simone Benaglia, Ravindra Thakkar, Jeffrey Comer, Ricardo Garcia
Summary: Hydration layers form on hydrophilic and hydrophobic crystalline surfaces, but on hydrophobic surfaces, water molecules are expelled and replaced by hydrocarbon molecules near the surface, creating a new interfacial layer.
Article
Chemistry, Physical
Paulo G. M. Mileo, Sven M. J. Rogge, Maarten Houlleberghs, Eric Breynaert, Johan A. Martens, Veronique Van Speybroeck
Summary: Research suggests that confining clathrates in nanoporous materials can enhance their stability, with key design criteria including large pore sizes, high ligand densities, and smooth pore walls.
JOURNAL OF MATERIALS CHEMISTRY A
(2021)
Article
Polymer Science
R. Bharath Venkatesh, Daeyeon Lee
Summary: The dynamics of confined polymers are influenced by factors such as entanglement, interfacial friction, and environmental conditions. This study investigates the motion of polydimethylsiloxane in silica nanoparticle packings and reveals the interplay of confinement, interfacial friction, and humidity on polymer dynamics.
Article
Polymer Science
R. Bharath Venkatesh, Daeyeon Lee
Summary: The dynamics of confined polymers are crucial for the properties and performance of nanoscale polymeric systems. This study reveals the reduced role of topological entanglements and the dominant role of interfacial friction in the dynamics of confined polymers.
Article
Chemistry, Physical
Souvik Math, Jianping Gao, Uzi Landman
Summary: The compositional, structural, and diffusional properties of equal-weight mixtures of liquid n-hexane and n-hexadecane films supported on atomically smooth and rough gold surfaces have been studied using temperature-controlled, canonical, molecular dynamics simulations. The preferential adsorption of n-hexadecane molecules near the solid surface has been observed. The selective molecular segregation effect is stronger on the smooth Au(111) surface, where pronounced layering is exhibited. Reduced diffusive motion is found near the solid surfaces, and the diffusion rate is higher for the hexane molecules on the smooth surface due to the formation of ordered domains.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Multidisciplinary Sciences
Limei Qin, Jie Gan, Dechao Niu, Yueqiang Cao, Xuezhi Duan, Xing Qin, Hao Zhang, Zheng Jiang, Yongjun Jiang, Sheng Dai, Yongsheng Li, Jianlin Shi
Summary: Developing effective methodologies to construct highly active catalytic sites for material engineering is attractive. A novel interfacial-confined coordination strategy was proposed to anchor Fe single atoms on defective carbon dots in a biocompatible mesoporous silica nanoreactor, showing efficient energy conversion capability under physical and biochemical stimuli. The highest photothermal conversion efficiency is proposed by theoretical DFT calculations, providing a scientific paradigm for versatile single atom nanotherapeutics for tumor therapy.
NATURE COMMUNICATIONS
(2022)
Article
Engineering, Mechanical
Chongpu Zhai, Shuwen Zhang, Hui Ji, Deheng Wei, Hengxu Song, Kaiyuan Liu, Minglong Xu
Summary: This study quantifies the impact of surface roughness on interfacial flexoelectricity during normal compression and oscillation. Through examining 3D-printed surfaces with different roughness features, the researchers found that the flexoelectric charge follows a power-law relationship with the compression load, and the exponent is positively correlated with the fractal dimension. Contact analyses reveal that the flexoelectric charge concentrates on larger microcontacts as compression continues, and rougher surfaces show less heterogeneity in flexoelectric polarizations. This study provides experimental measurements and explanations for interfacial flexoelectricity, highlighting its connection to surface structures and suggesting new approaches for contact evaluation and flexoelectricity enhancement.
EXTREME MECHANICS LETTERS
(2023)
Review
Mechanics
Daniel Chung, Nicholas Hutchins, Michael P. Schultz, Karen A. Flack
Summary: Reliable full-scale prediction of drag due to rough wall-bounded turbulent fluid flow remains a challenge, with at least 10% uncertainty. Recent advances have lowered barriers and are beginning to impact other multiphysical areas, promising increased predictive reliability.
ANNUAL REVIEW OF FLUID MECHANICS, VOL 53
(2021)
Review
Engineering, Environmental
Zhoujie Wang, Qiuyi Lu, Jingyi Wang, Jing Liu, Guangyi Liu, Wei Sun, Lei Xie, Qi Liu, Hongbo Zeng
Summary: Hydrophobic interactions are crucial in various mineral systems, affecting processes such as water treatment, particle separation, and self-cleaning or electrocatalysis in functional materials. The quantification and modulation of these interactions at the mineral/water interface provide insights into the underlying mechanisms of such particles’ interfacial processes. This review focuses on the nanomechanical understanding of hydrophobic interactions on mineral surfaces, discussing topics such as water structure, mineral surface wettability, agglomeration, bubble attachment, and adsorption of organics. The review also highlights the recent advances in using stimuli-responsive polymers to modulate hydrophobic interactions and identifies future research perspectives.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Multidisciplinary Sciences
Benbing Shi, Xiao Pang, Shunning Li, Hong Wu, Jianliang Shen, Xiaoyao Wang, Chunyang Fan, Li Cao, Tianhao Zhu, Ming Qiu, Zhuoyu Yin, Yan Kong, Yiqin Liu, Mingzheng Zhang, Yawei Liu, Feng Pan, Zhongyi Jiang
Summary: The idea of spatial confinement has gained widespread interest in various applications. This study demonstrates the confinement of a short hydrogen-bond (SHB) network on the surface of ionic covalent organic framework (COF) membranes. By decorating the surface with densely and uniformly distributed hydrophilic ligands, water molecules are allocated to each ligand, forming water-hydronium domains and creating an interconnected SHB network. Experimental and theoretical evidence shows that this confined SHB network exhibits an unprecedented ultrahigh proton conductivity.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Lisa M. Pietrek, Lukas S. Stelzl, Gerhard Hummer
Summary: Disordered proteins and nucleic acids are important in cellular function and disease. This review discusses recent advances in computationally exploring the dynamics of flexible biomolecules. While molecular dynamics simulation has improved, large-scale computing resources and validation are needed for simulating full-length disordered biopolymers. Hierarchical chain growth is a computationally efficient alternative that combines chain fragments into detailed biomolecular structures. Applications to neurodegeneration-linked proteins highlight the use of hierarchical chain growth, and connections to AI-based structural modeling are also discussed.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Soeren von Buelow, Mateusz Sikora, Florian E. C. Blanc, Roberto Covino, Gerhard Hummer
Summary: Since the start of the COVID-19 pandemic, the emergence of new variants has hindered the effectiveness of vaccines and made achieving herd immunity difficult. However, through molecular dynamics simulations of a SARS-CoV-2 spike protein model, researchers have found that the accessibility of antibodies to regions beyond the glycan shield can predict mutated positions in important variants like Omicron. This understanding of viral evolution and immune defense can help in predicting future mutation activity and escape from antibody-based immune responses.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Chemistry, Physical
Balazs Fabian, Sebastian Thallmair, Gerhard Hummer
Summary: Artificial temperature gradients were observed in MD simulations of phase-separating ternary lipid mixtures using the Martini 2 force field. This was traced back to insufficiently converged bond length constraints caused by default settings and time steps in the linear constraint solver (LINCS). By optimizing the constraint scaffold of cholesterol with equimomental arrangement of virtual sites, the bond constraint convergence can be accelerated while maintaining the original cholesterol force field and dynamics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Jakob Tomas Bullerjahn, Soren von Bulow, Maziar Heidari, Jerome Henin, Gerhard Hummer
Summary: In molecular dynamics simulations, the size and shape of the simulation box may vary over time. Unbounded position displacements can occur when rescaling the box by the barostat for particle images far from the origin. This necessitates careful trajectory unwrapping and rewrapping methods for accurate calculations of translational diffusion coefficients.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Multidisciplinary Sciences
Miao Yu, Maziar Heidari, Sofya Mikhaleva, Piau Siong Tan, Sara Mingu, Hao Ruan, Christopher D. Reinkemeier, Agnieszka Obarska-Kosinska, Marc Siggel, Martin Beck, Gerhard Hummer, Edward A. Lemke
Summary: This study investigates the conformation of FG nucleoporin NUP98 inside the mammalian nuclear pore complex. The researchers used synthetic biology and time-resolved fluorescence microscopy to directly probe the structure in live cells and permeabilized cells. They found that the channel provides a "good solvent" environment, allowing the FG domain to adopt expanded conformations and control transport between the nucleus and cytoplasm.
Article
Multidisciplinary Sciences
Alexis Gonzalez, Adriana Covarrubias-Pinto, Ramachandra M. Bhaskara, Marius Glogger, Santosh K. Kuncha, Audrey Xavier, Eric Seemann, Mohit Misra, Marina E. Hoffmann, Bastian Braeuning, Ashwin Balakrishnan, Britta Qualmann, Volker Doetsch, Brenda A. Schulman, Michael M. Kessels, Christian A. Huebner, Mike Heilemann, Gerhard Hummer, Ivan Dikic
Summary: The endoplasmic reticulum (ER) can be remodeled through a selective autophagy pathway called ER-phagy. This study identified that ubiquitination of the ER-phagy receptor FAM134B promotes receptor clustering and binding to LC3B, stimulating ER-phagy. The results reveal the importance of ubiquitination in enhancing ER-phagy and controlling ER remodeling.
Article
Multidisciplinary Sciences
Hector Foronda, Yangxue Fu, Adriana Covarrubias-Pinto, Hartmut T. Bocker, Alexis Gonzalez, Eric Seemann, Patricia Franzka, Andrea Bock, Ramachandra M. M. Bhaskara, Lutz Liebmann, Marina E. E. Hoffmann, Istvan Katona, Nicole Koch, Joachim Weis, Ingo Kurth, Joseph G. G. Gleeson, Fulvio Reggiori, Gerhard Hummer, Michael M. M. Kessels, Britta Qualmann, Muriel Mari, Ivan Dikic, Christian A. A. Huebner
Summary: Membrane-shaping proteins containing reticulon homology domains are crucial for dynamic remodelling of the endoplasmic reticulum (ER). FAM134B is an example of such a protein, which mediates the degradation of ER sheets through a process called selective autophagy (ER-phagy) by binding to LC3 proteins. Mutations in FAM134B result in a neurodegenerative disorder in humans.
Article
Biochemistry & Molecular Biology
Di Wu, Ahmad R. R. Mehdipour, Franziska Finke, Hojjat G. G. Goojani, Roan R. R. Groh, Tamara N. N. Grund, Thomas M. B. Reichhart, Rita Zimmermann, Sonja Welsch, Dirk Bald, Mark Shepherd, Gerhard Hummer, Schara Safarian
Summary: CydDC is a protein transporter responsible for the transport of heme, a redox-active cofactor, from the cytoplasm to the respiratory chain complexes, playing a crucial role in cellular respiration. Through the integrated use of cellular, biochemical, structural and computational methods, the structure and function of CydDC, as well as its mechanism in the functional maturation of cytochrome bd, have been revealed.
NATURE CHEMICAL BIOLOGY
(2023)
Correction
Multidisciplinary Sciences
Rong Zhu, Daniel Canena, Mateusz Sikora, Miriam Klausberger, Hannah Seferovic, Ahmad Reza Mehdipour, Lisa Hain, Elisabeth Laurent, Vanessa Monteil, Gerald Wirnsberger, Ralph Wieneke, Robert Tampe, Nikolaus F. Kienzl, Lukas Mach, Ali Mirazimi, Yoo Jin Oh, Josef M. Penninger, Gerhard Hummer, Peter Hinterdorfer
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Luis Borges-Araujo, Ana C. Borges-Araujo, Tugba Nur Ozturk, Daniel P. Ramirez-Echemendia, Balazs Fabian, Timothy S. Carpenter, Sebastian Thallmair, Jonathan Barnoud, Helgi I. Ingolfsson, Gerhard Hummer, D. Peter Tieleman, Siewert J. Marrink, Paulo C. T. Souza, Manuel N. Melo
Summary: Cholesterol plays a crucial role in biomembranes by regulating various properties of lipid bilayers. Martini 3 model offers significant improvements in interaction balance and molecular packing, and includes a new cholesterol model that mitigates some limitations of its predecessor.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Clara Lettl, Franziska Schindele, Ahmad Reza Mehdipour, Thomas Steiner, Diana Ring, Ruth Brack-Werner, Baerbel Stecher, Wolfgang Eisenreich, Ursula Bilitewski, Gerhard Hummer, Matthias Witschel, Wolfgang Fischer, Rainer Haas
Summary: Respiratory complex I plays an important role in cellular respiration of both eukaryotic cells and bacteria. The inhibition of complex I by mitochondrial complex I inhibitors can selectively kill Helicobacter pylori, a Gram-negative bacterial pathogen, while leaving other bacteria unaffected. The unique composition of the quinone-binding pocket in H. pylori complex I is responsible for this hypersensitivity, suggesting the potential of developing complex I inhibitors as narrow-spectrum antimicrobial agents against H. pylori.
CELL CHEMICAL BIOLOGY
(2023)
Article
Computer Science, Interdisciplinary Applications
Hendrik Jung, Roberto Covino, A. Arjun, Christian Leitold, Christoph Dellago, Peter G. Bolhuis, Gerhard Hummer
Summary: A machine learning algorithm accelerates the sampling of rare assembly events, uncovers their mechanisms, extrapolates them across chemical and thermodynamic space, and condenses the learned assembly mechanisms into a human-interpretable form.
NATURE COMPUTATIONAL SCIENCE
(2023)
Article
Chemistry, Physical
Hyuntae Kim, Balazs Fabian, Gerhard Hummer
Summary: This study highlights the issues of membrane deformation and pressure imbalance in molecular dynamics simulations when using default parameters. The problems are mainly caused by missed nonbonded interactions and unbalanced pressure tensor, which result from improper parameter settings.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Multidisciplinary Sciences
Amir Pandi, David Adam, Amir Zare, Van Tuan Trinh, Stefan L. Schaefer, Marie Burt, Bjorn Klabunde, Elizaveta Bobkova, Manish Kushwaha, Yeganeh Foroughijabbari, Peter Braun, Christoph Spahn, Christian Preusser, Elke Pogge von Strandmann, Helge B. Bode, Heiner von Buttlar, Wilhelm Bertrams, Anna Lena Jung, Frank Abendroth, Bernd Schmeck, Gerhard Hummer, Olalla Vazquez, Tobias J. Erb
Summary: This study demonstrates the potential of using deep learning and cell-free protein synthesis for the rapid and cost-effective production and testing of bioactive peptides. Through computational methods and experimental validation, the authors identified 30 functional peptides, including six with broad-spectrum activity against drug-resistant pathogens.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Fluids & Plasmas
Jakob Tomas Bullerjahn, Balazs Fabian, Gerhard Hummer
Summary: This article presents an algorithm for generating random 4D rotation matrices, which has applications in robotics, computer vision, and rigid-body mechanics. The algorithm enables efficient sampling of the SO(4) group of 4D rotations.