Article
Thermodynamics
William A. Sirignano
Summary: A new sub-grid flamelet model based on a steady-state, viscous vortex layer has been developed. The model imposes a compressive strain orthogonal to both vorticity and shear force, resulting in the stretching of vorticity in the direction orthogonal to the shear strain plane. The model has unique features, including the ability to determine non-premixed flames, premixed flames, or multi-branched flame structures. Despite being a two-dimensional model, it considers three components of velocity and addresses variable density effects. The importance of the compressive strain rate and the strong influence of vorticity on scalar profiles are highlighted. The model expands the available collection for studying vortical configurations in turbulent combustion.
COMBUSTION AND FLAME
(2022)
Article
Construction & Building Technology
Qiang Zhang, Wei He, Hong-Ying Wang, Ri-Cheng Liu, Meng-Meng Lu, Bin-Song Jiang
Summary: This paper presents an analytical finite strain solution for cavity expansion in strain-hardening and/or softening Mohr-Coulomb soil, considering the evolutions of material parameters. The study found that for the same cavity expansion, the required cavity pressure for strain-hardening and/or softening soils may be larger or smaller than that of elasto-perfectly plastic soils.
TUNNELLING AND UNDERGROUND SPACE TECHNOLOGY
(2021)
Article
Materials Science, Multidisciplinary
Michael E. Kassner, Roya Ermagan
Summary: This paper discusses the phenomenon of softening in metals and alloys during torsional deformation, and explores the relationship between softening and texture development, focusing on cases of BCC and HCP. The authors analyze the basis for torsional softening in BCC steel and HCP Zr, presenting a novel concept that has not been previously addressed in the literature.
Article
Engineering, Marine
Shujin Zhou, Mi Zhou, Yinghui Tian, Xihong Zhang
Summary: In this study, a large deformation finite-element (LDFE) model is established to investigate the penetration behavior of helical piles, considering the strain rate effect and strain softening effect in soil. The numerical model is validated by comparing with centrifuge results. Parametric studies show that the penetration behavior of helical piles is significantly influenced by the strain rate and strain softening of soil. The theoretical model for predicting torque requirements is extended to account for the strain rate and strain softening effect.
Article
Biochemistry & Molecular Biology
Anupam Mondal, Arnab Bhattacherjee
Summary: DNA morphology is influenced by environmental conditions and closely related to its function. Sigma-DNA, with a well-defined extended conformation, consists of triplets of nucleobases that facilitate DNA-binding protein recognition. Proteins show a preference for triplet formation, which enhances the efficiency of DNA base recognition.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Materials Science, Multidisciplinary
Maximilian Koehler, Daniel Balzani
Summary: A new relaxation approach is proposed to describe stress and strain softening at finite strains. The model constructs a convex hull to represent damage, allowing for the homogenization of a microstructure bifurcated in weakly and strongly damaged phases. The strongly damaged phase is allowed to elastically unload and its volume fraction increases within the convexified regime, enabling strain-softening. The proposed approach ensures mesh-independent structural simulations without additional length-scale parameters or nonlocal quantities.
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS
(2023)
Article
Materials Science, Multidisciplinary
Jian Li, Hannah Varner, Tal Cohen
Summary: The necking instability is a precursor to tensile failure and rupture of materials. It can exhibit periodic necking and fragmentation when confined to a substrate or embedded in a matrix. Necking in hyperelastic materials is not well understood, but there has been a renewed interest in its role for the advancement of fabrication processes and to explain fragmentation phenomena.
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS
(2023)
Article
Engineering, Manufacturing
Dong Zhang, Xiao-Ming Zhang, Guang-Chao Nie, Zheng-Yan Yang, Han Ding
Summary: This study attempts to develop a methodology to understand and identify plastic deformation behaviors during cutting tests, utilizing high-speed filming and induction preheating. By varying the rake angle, cutting velocity, and initial workpiece temperature, different levels of strain, strain rate, and temperature are achieved, providing insights into material behaviors that can be further used in numerical machining models.
INTERNATIONAL JOURNAL OF MACHINE TOOLS & MANUFACTURE
(2021)
Article
Multidisciplinary Sciences
Estefania Vidal-Henriquez, David Zwicker
Summary: The study presents a theoretical description of droplets growing in an elastic matrix, revealing that large droplets only form when cavitation occurs, stabilizing the size and position of smaller droplets and increasing in density with faster cooling. The model also indicates how adjusting cooling protocols and nucleation site density affects droplet size distribution.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Computer Science, Interdisciplinary Applications
Chunlei Li, Long Yu, Xianjing Kong, Heyue Zhang
Summary: This study simulated the continuous penetration of a spherical penetrometer (ball) into softening and rate-dependent soil, revealing three stages from shallow failure mechanism to deep flow-round mechanism. The effects of strain rate and softening parameters on the failure mechanism and the evolved bearing factor profile were investigated. The dimensionless soil strength sum /gamma ' D and the frictional condition of the soil-ball interface were explored as well. Empirical formulas were developed to estimate the critical depths of the ball penetration test. A practical interpretation framework, incorporating the effects of strain rate and softening, was developed to assess the soil undrained shear strength using the ball penetrometer.
COMPUTERS AND GEOTECHNICS
(2023)
Article
Engineering, Ocean
Chunlei Li, Long Yu, Xianjing Kong, Yunrui Han
Summary: Pipe-soil interaction is crucial for deep-water pipeline systems as it affects their structural behavior and integrity. The pipe embedment plays a significant role in determining the boundary conditions and subsequently influencing the pipe-soil interaction. In this study, a robust finite-element model using the Remeshing and Interpolation Technique with Small Strain (RITSS) method was developed for vertical penetration of pipelines in clay. The model discussed the development mechanism of soil shear bands during pipeline penetration and explored the effects of pipeline roughness on shear strength degradation and enhancement. Parametric analysis also examined the effects of soil buoyancy, soil strength gradient, strain softening, and strain rate on penetration resistance. A validated evaluation framework for penetration resistance was developed based on the sensitivity of each parameter, which can provide valuable guidance for designing vertical penetration of pipelines in deep-water engineering.
APPLIED OCEAN RESEARCH
(2023)
Article
Engineering, Ocean
Shujin Zhou, Mi Zhou, Yinghui Tian, Xihong Zhang
Summary: In this study, a numerical model is established to investigate the soil flow mechanism of caissons with pad-eye stiffeners. The soil strain softening effect is considered. The study finds that the soil failure mechanisms and penetration resistances of locally stiffened caissons at the pad-eye are significantly different from unstiffened caissons or caissons with interval rings. A simplified flow mechanism is proposed and approximating expressions are derived for predicting the penetration resistance of the caisson.
APPLIED OCEAN RESEARCH
(2022)
Article
Polymer Science
Chao Zhang, Songlin Xu, Lei Zhang
Summary: This paper characterizes and models the mechanical behavior of partially crystalline Poly-Ether-EtherKetone, focusing on temperature softening, strain softening, and strain hardening behavior. A modified constitutive model is proposed, which shows good capability in predicting stress-strain curves at different deformation conditions. Further application of the model in finite element simulation in extreme conditions is recommended.
Article
Polymer Science
Xinke Zhong, Yihu Song, Qiang Zheng
Summary: In this study, the Payne effect and Mullins effect of unfilled and silica filled butadiene rubber (BR) vulcanizates were systematically investigated. It was found that the critical strain amplitude for the onset of Payne effect during large-amplitude oscillation shear is closely related to the storage modulus in the linear viscoelastic region. In cyclic tension deformations, the recovery hysteresis energy and accumulating softening energy are involved in the local deformation of the rubber matrix, which is promoted by the filler phase. These findings provide insights for optimizing the performance of rubber nanocomposite products by controlling the nonideal network structure of the viscoelastic rubber matrix.
Article
Polymer Science
Weiqin Tang, Dayong Li, Yinghong Peng, Peidong Wu
Summary: The study investigates the mechanism of shear band formation and evolution in amorphous glassy polymers, and finds that the initiation and propagation of shear bands are caused by intrinsic strain softening. Shear bands form and propagate during forward shearing, but gradually disappear during reverse shearing. Furthermore, shear bands cannot be recovered through reverse straining during plastic deformation.
Article
Chemistry, Physical
Adnan Choudhary, Christopher Maffeo, Aleksei Aksimentiev
Summary: Modeling and simulation play a crucial role in the development of nanopore sensing systems. The inability of the current signal to provide direct information about the chemical structure of biomolecules is a limitation of nanopore sensing. To overcome this, coarse-grained and all-atom molecular dynamics simulations are used to characterize the nanopore translocation process. However, traditional simulations have limitations in predicting ionic current blockades with atomic resolution. This study describes a multi-resolution framework for modeling the passage of DNA molecules and nanostructures through synthetic nanopore systems, providing accurate modeling capability to research laboratories without access to supercomputers.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
S. Kasra Tabatabaei, Bach Pham, Chao Pan, Jingqian Liu, Shubham Chandak, Spencer A. Shorkey, Alvaro G. Hernandez, Aleksei Aksimentiev, Min Chen, Charles M. Schroeder, Olgica Milenkovic
Summary: Researchers have developed a prototype DNA data storage system that uses an extended molecular alphabet to differentiate between natural and chemically modified nucleotides. They also demonstrated the capability of single-molecule sequencing using a neural network architecture, achieving an accuracy exceeding 60%.
Article
Multidisciplinary Sciences
David Winogradoff, Han-Yi Chou, Christopher Maffeo, Aleksei Aksimentiev
Summary: This study combines coarse-grained simulations and a theoretical model to elucidate the microscopic mechanism governing the selectivity of passive, unassisted transport through the nuclear pore complex. The model reproduces the energetics and kinetics of permeation solely from statistics of transient voids within the disordered mesh, enabling exploration of alternative NPC architectures.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Yi Li, Christopher Maffeo, Himanshu Joshi, Aleksei Aksimentiev, Brice Menard, Rebecca Schulman
Summary: This study demonstrates the design of micrometer-long, 7-nm-diameter DNA nanochannels that can be used for molecular transport. The channels eliminate permeation through channel walls and can interface with living cells.
Article
Chemistry, Multidisciplinary
Kaikai Chen, Adnan Choudhary, Sarah E. Sandler, Christopher Maffeo, Caterina Ducati, Aleksei Aksimentiev, Ulrich F. Keyser
Summary: High-resolution analysis of biomolecules has greatly advanced biosensing, but there are limited methods available for high-resolution analysis of unlabeled single molecules in their native states. In this work, label-free electrical sensing of single molecules with nanometer resolution is demonstrated using a narrow solid-state nanopore. The super-resolution ability is attributed to the enhancement of the electric field at the tip of the nanopore induced by nanostructures. This work presents a general approach to improve the resolution of single-molecule nanopore sensing and has implications for label-free high-resolution DNA sequence mapping and digital information storage.
ADVANCED MATERIALS
(2023)
Article
Biotechnology & Applied Microbiology
Luning Yu, Xinqi Kang, Fanjun Li, Behzad Mehrafrooz, Amr Makhamreh, Ali Fallahi, Joshua C. Foster, Aleksei Aksimentiev, Min Chen, Meni Wanunu
Summary: The electrical current blockade caused by a peptide or protein passing through a nanopore can be used as a fingerprint for molecule identification in biosensor applications. This study presents an enzyme-free method for slow, unidirectional transport of full-length proteins through nanopores. By using a chemically resistant biological nanopore, alpha-hemolysin, and a high concentration guanidinium chloride buffer, protein transport can be propelled by electroosmotic effect. The translocation dynamics of proteins resemble that of single-stranded DNA, and single-translocation events contain enough information for orientation and identity determination with over 90% accuracy using a supervised machine-learning classifier.
NATURE BIOTECHNOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Christopher Maffeo, Lauren Quednau, James Wilson, Aleksei Aksimentiev
Summary: Flowing fluid past chiral objects has been used to power rotary motion in man-made machines for centuries. In nanoscale biological or chemical systems, rotary motion is generated by biasing Brownian motion through cyclic chemical reactions. In this study, we demonstrate that a chiral biological molecule (DNA or RNA duplex) rotates unidirectionally at billions of revolutions per minute when an electric field is applied along the duplex, with the rotation direction determined by the duplex's chirality. The rotation is powered by the drag force of the electro-osmotic flow, mimicking the operating principle of a macroscopic turbine at the nanoscale.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Physical
Kumar Sarthak, David Winogradoff, Yingda Ge, Sua Myong, Aleksei Aksimentiev
Summary: Proteins with disordered regions are important for cellular signaling and biological condensates, but mutations can lead to neurodegenerative diseases. Molecular dynamics simulations were used to study the effects of different force fields on the structure and dynamics of a protein called FUS. The simulations showed that certain force fields produced conformations within the experimental range and also influenced the stability of RNA-protein complexes. The findings suggest that a combination of protein and RNA force fields can provide an optimal description of proteins with both structured and disordered regions and their interactions with RNA.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Siddharth Krishnan, Aleksei Aksimentiev, Stuart Lindsay, Dmitry Matyushov
Summary: Single-molecule measurements reveal that proteins without redox cofactors can still exhibit electrical conductance over nanometer scale distances. This is surprising considering the expected time scale for electron transport based on hopping rates and energy barriers. However, molecular dynamics simulations combined with an electron transfer theory show that the unique molecular configurations of non-redox-active proteins allow for long-range conductivity with low reorganization energies. These findings are supported by experimental current decay calculations.
ACS PHYSICAL CHEMISTRY AU
(2023)
Review
Chemistry, Multidisciplinary
Xiaojun Wei, Tadas Penkauskas, Joseph E. Reiner, Celeste Kennard, Mark J. Uline, Qian Wang, Sheng Li, Aleksei Aksimentiev, Joseph W. F. Robertson, Chang Liu
Summary: Biotechnological innovations have advanced large-scale protein studies, but current methods for identifying and quantifying individual proteins are insufficient for single-molecule protein sequencing. Nanopore-inspired systems have been developed for genome sequencing, and are now emerging as tools for protein identification and analysis, with potential for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors for protein sequencing, including amino acid identification, controlled translocation of peptides and proteins, and device and algorithm development supported by simulations. The review highlights the need for collaborative efforts across multiple disciplines to enable practical implementation of nanopore-based protein sequencing.
Correction
Biotechnology & Applied Microbiology
Luning Yu, Xinqi Kang, Fanjun Li, Behzad Mehrafrooz, Amr Makhamreh, Ali Fallahi, Joshua C. Foster, Aleksei Aksimentiev, Min Chen, Meni Wanunu
NATURE BIOTECHNOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Xin Shi, Anna-Katharina Pumm, Christopher Maffeo, Fabian Kohler, Elija Feigl, Wenxuan Zhao, Daniel Verschueren, Ramin Golestanian, Aleksei Aksimentiev, Hendrik Dietz, Cees Dekker
Summary: In this study, we experimentally demonstrate the feasibility of developing functional synthetic turbines at the nanoscale by rationally designing nanoscale DNA origami turbines. These turbines can utilize transmembrane electrochemical potentials to rotate autonomously and operate in physiological conditions. This research opens new possibilities for engineering active robotics at the nanoscale.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Physical
Prabhat Tripathi, Behzad Mehrafrooz, Aleksei Aksimentiev, Sophie E. Jackson, Martin Gruebele, Meni Wanunu
Summary: This study investigates the behavior of knotted protein structures during translocation through a pore. Using single molecule nanopore experiments and all-atom MD simulations, the researchers observed an unusual behavior in which the rate of translocation plateaus or slows down as the electric potential driving the reaction increases. This study sheds light on the influence of topology on the forced translocation of knotted proteins.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Merle Scherf, Florian Scheffler, Christopher Maffeo, Ulrich Kemper, Jingjing Ye, Aleksei Aksimentiev, Ralf Seidel, Uta Reibetanz
Summary: The development of DNA origami technique has inspired the use of three-dimensional DNA cages for targeted drug delivery. This study presents a method using DNA origami nanotubes for efficient loading and retention of cargo molecules within the DNA cages.
Article
Chemistry, Multidisciplinary
Prabhat Tripathi, Morgan Chandler, Christopher Michael Maffeo, Ali Fallahi, Amr Makhamreh, Justin Halman, Aleksei Aksimentiev, Kirill A. Afonin, Meni Wanunu
Summary: This study characterizes and distinguishes RNA fiber structures with different degrees of branching using solid-state nanopore experiments and simulations. It is found that fibers with more branches produce longer and deeper ionic current blockades. Additionally, the study shows that the kissing loop interactions in the fibers are resistant to heating.
