Article
Chemistry, Multidisciplinary
Dor Zaguri, Manuela R. Zimmermann, Georg Meisl, Aviad Levin, Sigal Rencus-Lazar, Tuomas P. J. Knowles, Ehud Gazit
Summary: The study found that the aggregation propensity of three phenylalanine-containing molecules increases significantly with size, with triphenylalanine being the most aggregation-prone species under experimental conditions. In the context of classical nucleation theory, this increase in aggregation propensity is attributed to the larger free energy decrease upon aggregation of larger peptides, and not to the presence/absence of a peptide bond per se. This work provides insights into the aggregation processes of chemically simple systems and suggests that both backbone-containing peptides and backbone-lacking amino acids assemble through a similar mechanism, supporting the classification of amino acids in the continuum of amyloid-forming building blocks.
Article
Multidisciplinary Sciences
Alexander Hensley, William M. Jacobs, W. Benjamin Rogers
Summary: DNA-coated colloids can self-assemble into various crystal structures, and we have used microfluidics to quantify the kinetics of crystallization. Our study shows that classical theories can accurately predict nucleation and growth rates, and we have successfully designed large single crystals with specific structural coloration.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Polymer Science
Yilong Liao, Li Pan, Zhe Ma, Dario Cavallo, Guoming Liu, Dujin Wang, Alejandro J. Mueller
Summary: The influence of a novel comonomer ODPA on the crystallization and self-nucleation behavior of isotactic polypropylene copolymers was studied. The results showed that ODPA incorporation significantly slowed down the crystallization kinetics and led to a sharp increase in nucleation density, resulting in smaller spherulitic superstructures. Moreover, ODPA induced a strong melt memory effect that persisted even above the equilibrium melting temperature for certain ODPA content ranges.
Article
Chemistry, Multidisciplinary
Hossein Eslami, Florian Mueller-Plathe
Summary: The self-assembly of triblock Janus particles and the relative stability of different lattices were simulated. The nucleation process consists of two steps: the formation of a compact and disordered liquid cluster, followed by the reorientation of particles to form crystalline nuclei. The nucleation barriers for pyrochlore and perovskite were similar to previously studied 2D kagome lattices, while the barrier for diamond was larger.
Article
Chemistry, Physical
Meng Wang, Jingkang Wang, Na Wang, Wenxi Song, Xin Huang, Ting Wang, Hongxun Hao
Summary: Nucleation, as a crucial process in crystallization, determines the physicochemical properties of crystal products. The mechanism of nucleation is not fully understood due to the complexity of molecular assembly. In this study, the connection between nucleation kinetics and solution chemistry was investigated using 3,5-dinitrobenzoic acid (DNBA) as a model compound. The existing form of DNBA molecules in solutions was analyzed, and the relationship between molecular existing form and nucleation kinetics was revealed. A possible nucleation mechanism of DNBA molecules in solution was proposed.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Jan Pille, Antonio Aloi, Duc H. T. Le, Ilia Vialshin, Nathalie van de Laar, Kirsten Kevenaar, Maarten Merkx, Ilja K. Voets, Jan C. M. van Hest
Summary: This study introduces a novel pathway-dependent assembly method based on stimulus-responsive polymers, which can form monodisperse and stable polymeric particles under specific heating conditions. This method shows high efficiency in encapsulating cargo, such as fluorescent proteins and bioluminescent enzymes, and maintaining their function within cells.
Article
Chemistry, Multidisciplinary
Priyanka, Surinder Kaur Brar, Subhabrata Maiti
Summary: Understanding the changes in functional properties of synthetic nanoscale self-organized systems by introducing exogenous modules has broad applications in designing responsive biomimic materials. In this study, a substrate-driven nanoscale vesicular assembly was developed, and it was found that nucleotides interact differently with the assembly, leading to alterations in its functional properties.
Article
Chemistry, Multidisciplinary
Pin-Wei Lee, Adrian Saura-Sanmartin, Christoph A. Schalley
Summary: This study presents a supramolecular assembly method for superhydrophobic coatings using a low molecular weight gelator and acrylate polymers, resulting in scratch-resistant and transparent coatings. The incorporation of covalent polymers improves the mechanical resistance and optical transparency of the coatings while maintaining their water and oil repellency.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Chemistry, Applied
Jihyun Kim, Seon-Min Oh, Hui-Yun Kim, Jong-Hyun Choi, Jae-Sung Shin, Ji-Eun Bae, Sang-Jin Ye, Moo-Yeol Baik
Summary: The self-assembly kinetics of short-chain glucan aggregates prepared under isothermal conditions were investigated. The formation and crystallization rates were fastest at 4°C and 20°C. Nucleation allowed for the formation of aggregates at 60°C, and increased yield at all temperatures. All aggregates exhibited B-type crystal patterns and nanosized particles (<500 nm). Manipulation of the nucleation step is expected to be an effective method for increasing yield and producing aggregates at high temperature.
Article
Chemistry, Multidisciplinary
Alexander Cumberworth, Daan Frenkel, Aleks Reinhardt
Summary: Nucleation is the rate-determining step in the kinetics of self-assembly processes. The importance of nucleation in DNA-origami self-assembly is unclear. Monte Carlo simulations of a lattice model of DNA origami revealed that some designs have a nucleation barrier, which disappears at lower temperatures. The height of the nucleation barrier depends on the coaxial stacking of adjacent staples, which can be modified with staple design. Creating or eliminating the nucleation barrier may have implications for optimizing assembly times, yields, and developing fast molecular sensors.
Article
Chemistry, Multidisciplinary
Zijian Zhou, Chao Du, Qianyu Zhang, Guocan Yu, Fuwu Zhang, Xiaoyuan Chen
Summary: By modulating the self-assembly of drug amphiphiles EB-CPT with the anticancer drug PTX, ultrahigh quality nanovesicles (NVs) were produced with high drug loading efficiency and content. The ECX NVs with EB-CPT:PTX weight ratio of 1:2 exhibited remarkable anticancer activity against cancer cells and improved tumor inhibition effect in vivo.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Engineering, Environmental
Lingyu Sun, Yu Wang, Xiaoxuan Zhang, Feika Bian, Luoran Shang, Yuanjin Zhao, Weijian Sun
Summary: This study introduces novel lubricant infused hierarchical porous surfaces with self-replenishing and self-reporting capacities inspired by the rapid replenishment of Nepenthes nectaries. These hierarchical inverse opal films exhibit liquid-repelling feature on liquids with different surface tensions and have favorable self-replenishment capacity for stable droplet manipulation. The structural colors from the periodic nanostructure could serve as an optical indicator to monitor the wettability of the surfaces.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Polymer Science
Thomas Babut, Mona Semsarilar, Marc Rolland, Damien Quemener
Summary: In this study, a waterborne approach was proposed to co-assemble peptide amphiphiles (PA) and polyelectrolytes into porous membranes with nanostructured networks. Various production methods were explored to shape the material and optimize the structure, leading to a membrane material in the ultrafiltration range with a pore radius of about 7.6 nm.
Article
Materials Science, Multidisciplinary
Yuefei Wang, Dongzhao Hao, Jiayu Liu, Qing Li, Zixuan Wang, Xi Rong, Wei Qi, Rongxin Su, Zhimin He
Summary: Researchers have found that self-assembling peptide nanofibril films can spontaneously form Fibonacci number spiral patterns, which are also commonly found in nature. By manipulating the nanofibers, various complex hierarchical structures can be formed.
SCIENCE CHINA-MATERIALS
(2022)
Article
Polymer Science
Qingquan Tang, Hao Ren, Zdravko Kochovski, Lisheng Cheng, Ke Zhang, Jiayin Yuan, Weiyi Zhang
Summary: The topological geometry of poly(ionic liquid)s has a strong influence on their self-assembly behaviors. This study investigates the effects of cyclic topology on poly(ionic liquid)s by preparing linear and cyclic copolymers and studying their self-assembly phenomena. The results show that the average size of cyclic copolymers nanospheres is 46.2% smaller than linear copolymers nano-assemblies. The authors speculate that the spherical aggregates are formed through a transition from micelles with gradient block-like structures.
MACROMOLECULAR CHEMISTRY AND PHYSICS
(2023)
Article
Chemistry, Physical
S. Ramirez-Hinestrosa, H. Yoshida, L. Bocquet, D. Frenkel
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Physics, Multidisciplinary
Shaltiel Eloul, Wilson C. K. Poon, Oded Farago, Daan Frenkel
PHYSICAL REVIEW LETTERS
(2020)
Article
Multidisciplinary Sciences
Jorge R. Espinosa, Jerelle A. Joseph, Ignacio Sanchez-Burgos, Adiran Garaizar, Daan Frenkel, Rosana Collepardo-Guevara
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Chemistry, Physical
Xipeng Wang, Simon Ramirez-Hinestrosa, Daan Frenkel
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Chemistry, Physical
S. W. Coles, E. Mangaud, D. Frenkel, B. Rotenberg
Summary: This study presents a method to further reduce the variance of force-based estimators by considering optimal linear combinations, which has been comparatively less explored in molecular simulations. The approach not only effectively reduces the variance, but also corrects a defect of the initial estimators, highlighting the underexplored potential of control variates in estimating observables from molecular simulations.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
H. A. Vinutha, Daan Frenkel
Summary: By utilizing a recently developed technique and different methods to calculate the solubility and chemical potential differences of amorphous solids, it is found that using the Jarzynski method for computing the chemical potential of components yields more accurate results for solubility and chemical potential calculations of glassy materials.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Vikram Khanna, Jamshed Anwar, Daan Frenkel, Michael F. Doherty, Baron Peters
Summary: This paper extends previous work on free energy calculations of crystals using a center of mass constraint and finite-size corrections, focusing on crystals with differing spring constants. By comparing free energies calculated with different spring constants, the theory is tested and the intrinsic finite-size effects are eliminated. The calculations help demonstrate the impact of these finite-size corrections on the absolute free energy of crystals.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
H. A. Vinutha, Daan Frenkel
Summary: The study demonstrates that plausible free-energy estimates of a Kob-Andersen glass can be obtained using the Jarzynski relation, which matches well with the extrapolated value of the supercooled liquid in the glassy regime. This finding is significant for the broader interest in the field of thermodynamic methods.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Yawei Liu, Jiachen Wei, Daan Frenkel, Asaph Widmer-Cooper
Summary: In this study, a coarse-grained model based on the DPD method was developed to investigate the aggregation of CTAB molecules on gold surfaces. The model can describe the structural changes of CTAB aggregates on gold surfaces and around gold nanorods, predicting the distribution of ligand density within the CTAB layer.
MOLECULAR SIMULATION
(2022)
Review
Physics, Condensed Matter
Simon Ramirez-Hinestrosa, Daan Frenkel
Summary: The paper uses a unified framework to describe diffusio-osmosis and reports non-equilibrium molecular dynamics (NEMD) on such systems. Different simulation methods are explored to highlight technical problems in calculations, with two NEMD methods used for diffusiophoresis.
EUROPEAN PHYSICAL JOURNAL B
(2021)
Article
Chemistry, Physical
Yagyik Goswami, Vishwas V. Vasisht, Daan Frenkel, Pablo G. Debenedetti, Srikanth Sastry
Summary: This study investigated the kinetics of crystallization in deeply supercooled liquid silicon using computer simulations and Stillinger-Weber potential. The research focused on the presence of free energy barriers to crystallization at state points near a liquid-liquid phase transition, providing strong evidence against the possibility of slow, spontaneous crystallization in those states. The results also discussed the effect of changes in the microscopic structure of the metastable liquid on the free energy barrier heights.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Alexander Cumberworth, Daan Frenkel, Aleks Reinhardt
Summary: Nucleation is the rate-determining step in the kinetics of self-assembly processes. The importance of nucleation in DNA-origami self-assembly is unclear. Monte Carlo simulations of a lattice model of DNA origami revealed that some designs have a nucleation barrier, which disappears at lower temperatures. The height of the nucleation barrier depends on the coaxial stacking of adjacent staples, which can be modified with staple design. Creating or eliminating the nucleation barrier may have implications for optimizing assembly times, yields, and developing fast molecular sensors.
Article
Physics, Multidisciplinary
Xipeng Wang, Jure Dobnikar, Daan Frenkel
Summary: In this study, we conducted simulations to test the Onsager reciprocity relations in a nonequilibrium steady state system. Our results demonstrate that these relations still hold true in the linear regime, even when the system is perturbed from a nonequilibrium steady state in a way that does not satisfy time-reversal symmetry. This suggests that the Onsager relations are applicable beyond their original range and may be relevant for transport in driven or active systems.
PHYSICAL REVIEW LETTERS
(2022)
Article
Chemistry, Physical
Shaltiel Eloul, Daan Frenkel
Summary: The study proposes a switchable nano-scale fluid pump, driven by exothermic surface reactions, which could be controlled electro-chemically. Simulations show that the simplicity of the pump design could make it attractive for micro/nano-fluidics applications.
Article
Physics, Fluids & Plasmas
H. A. Vinutha, Daan Frenkel