Article
Chemistry, Analytical
Xijian Lin, Yan He
Summary: This study investigates the effect of active urease system on the environment using high-speed dark-field imaging. The results show that the catalytic reaction has minimal impact on the physicochemical properties of the environment but can lead to the inhomogeneous distribution of enzymes in free solution.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Karol Liszka, Andrzej Grzybowski, Kajetan Koperwas, Marian Paluch
Summary: The study demonstrates that using an anisotropic model can better reflect the density scaling properties observed in experimental data, compared to previous use of isotropic models. By studying the dynamic scaling properties, the most appropriate scaling exponent values for a given anisotropy have been successfully determined, contributing to a better understanding of the density scaling idea. Therefore, it is recommended that future research on glass transition and supercooled liquids should employ anisotropic models.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Danh Nguyen, James Wu, Patrick Corrigan, Ying Li
Summary: This study investigates the mechanisms of lipid bilayer disruption by Janus nanoparticles (NPs) through computational simulations. The results reveal that the Janus balance and the concentration of charged phospholipids play significant roles in the interactions between Janus NPs and lipid bilayers. The study provides molecular insights into the selectivity of Janus NPs for negatively charged lipid membranes and highlights the importance of the anisotropic properties of Janus NPs in membrane disruption.
Article
Biochemistry & Molecular Biology
Danuta Kruk, Elzbieta Masiewicz, Sylwia Lotarska, Roksana Markiewicz, Stefan Jurga
Summary: H-1 spin-lattice relaxation experiments were conducted on a series of ionic liquids containing different alkyl chain lengths of bis(trifluoromethanesulfonyl)imide anion and cations. The results provided insights into the rotational and translational dynamics of the cations in comparison to molecular liquids, indicating a temperature-dependent ratio between the correlation times of these motions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Vaibhav Sharma, Florent Fessler, Fabrice Thalmann, Carlos M. Marques, Antonio Stocco
Summary: Measuring the rotational and translational Brownian motion of single spherical particles can reveal dissipations due to particle-environment interaction. The experiments conducted in this article demonstrate the measurement of in-plane translational and rotational drag coefficients for a single spherical Brownian particle. These drag coefficients are influenced by particle size, particle-wall distance, and viscous dissipations. Measurements on Janus particles close to solid walls and lipid bilayer membranes reveal that particle-wall distance and size can be determined by hydrodynamic models for particles close to walls. For particles partially wrapped by lipid membranes, when there is no strong binding interaction, translational and rotational drags are significantly larger compared to non-wrapped particles. The dissipations in the deformed membrane cap region also contribute strongly to the drag coefficients.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Biochemical Research Methods
Osama H. S. Al-Bahri, Bhaskarjyoti Borah, Mohammed Elzain, Srinivasa Rao Varanasi
Summary: This study investigates the translational and rotational dynamics of three isomers of trimethyl benzene under zeolite confinement using molecular dynamics simulations. The results show that one isomer is more facile in translation and rotational motion is more significant for the other two isomers. The differences in dynamic properties among these isomers are mainly caused by entropy.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Nanoscience & Nanotechnology
Wenxiong Cao, Yuan Liu, Pan Ran, Jie He, Shuang Xie, Jie Weng, Xiaohong Li
Summary: The study achieves precise and prompt thrombolysis through selective targeting to clots and efficient penetration into dense networks of thrombi using Janus rod (JR)-shaped micromotors.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Physics, Fluids & Plasmas
Luana S. Moreira, Douglas D. de Vargas, Mateus H. Kohler
Summary: The introduction of flexibility in water force fields during molecular dynamics simulations of nanoconfined water has a significant impact on viscosity, diffusion, and dipole orientation. The level of confinement and the choice of force-field family greatly influence the behavior of water molecules in nanoconfined systems.
Article
Physics, Fluids & Plasmas
Luana S. Moreira, Douglas D. de Vargas, Mateus H. Koehler
Summary: This study investigates the effects of introducing flexibility in water force fields on molecular dynamics simulations of nanoconfined water. The results show that viscosity, diffusion, and dipole orientation are greatly influenced by the flexibility and the family of force fields used.
Article
Biochemistry & Molecular Biology
Arne Werner
Summary: Diffusion is an inevitable prerequisite for ribonucleic acids to regulate gene expression and perform gene editing. The empirical models derived in this study accurately predict the three-dimensional translational and rotational diffusion velocities of RNA.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Nanoscience & Nanotechnology
Wei Li, Jun Ma, Santiago Garcia, Chongjie Gao, Ruochen Liu, Jingjing Qiu, Feng Zhao, Shiren Wang
Summary: The controllable aggregation of nanoparticles in solution is achieved through anisotropic semishell nanostructure, showing great potential for noninvasive photothermal therapy.
ACS APPLIED NANO MATERIALS
(2022)
Article
Chemistry, Physical
Margherita Mele, Roberto Covino, Raffaello Potestio
Summary: This study addresses the problem of coarsening the conformational space of proteins in molecular dynamics simulations. Using an information-theoretical framework, the researchers identified the optimal resolution level that balances simplicity and informativeness, and discovered that clustering methods inducing an ultrametric structure in the low-resolution space are the most physically accurate. The proposed strategy has applicability beyond computational biophysics and can be a valuable tool for extracting useful information from large datasets.
Article
Materials Science, Multidisciplinary
Ziquan Guo, Xiaobao Li, Meiqin Wang, Changzheng Cheng
Summary: The mechanical properties of single-walled Janus MoSSe nanotubes were investigated using classic molecular dynamics simulations. The study explored the elastic and plastic responses of the nanotubes under various loadings and temperatures, and observed phase transition behavior in armchair nanotubes under tensile loading at low temperatures. Fracture and buckling behaviors were analyzed, and the dependence of mechanical properties on size, chirality, and temperature was presented. The results provide valuable insights for the sustainability of nanoscale electronic devices based on semiconducting MoSSe nanotubes.
MECHANICS OF MATERIALS
(2023)
Article
Physics, Fluids & Plasmas
Siddharth Rajupet, Aidin Rashidi, Christopher L. Wirth
Summary: In this study, semianalytic equations were developed to accurately calculate the potential landscape of a Janus particle with nonuniform coating thickness above a solid boundary, including van der Waals interactions. The effects of both nonuniform coating thickness and van der Waals interactions significantly influence the potential landscape of the particle, particularly in high ionic strength solutions. The equations developed facilitate a more simple, accurate, and less computationally expensive characterization of conservative interactions experienced by a confined Janus particle than previous methods.
Article
Chemistry, Physical
Xianyu Song, Hongchao Liu, Xianli Duan, Qi Hu, Kezhong Liang, Tingzhen Li, Shuangliang Zhao, Honglai Liu
Summary: This study investigates the dynamics and thermodynamics of spontaneously translocating graphene quantum dots (GQDs) during cellular translocation. The findings reveal the competitive coordination between hydrophobic associations and hydrogen-bondings, which dictate the pathway and thermodynamic states for cellular translocation. A translocational phase diagram is drawn, and the importance of intermolecular mechanochemistry in energy transduction and nanomechanical interactions is discovered.
APPLIED SURFACE SCIENCE
(2023)
Article
Materials Science, Multidisciplinary
Nikolai V. Priezjev
COMPUTATIONAL MATERIALS SCIENCE
(2020)
Article
Materials Science, Multidisciplinary
Nikolai V. Priezjev
Article
Materials Science, Multidisciplinary
Nikolai V. Priezjev
METALLURGICAL AND MATERIALS TRANSACTIONS A-PHYSICAL METALLURGY AND MATERIALS SCIENCE
(2020)
Article
Materials Science, Ceramics
Nikolai V. Priezjev
Summary: This study investigates the influence of static stress and alternating loading direction on the potential energy and mechanical properties of amorphous alloys using molecular dynamics simulations. It was found that at sufficiently large values of static stress, the binary glass becomes rejuvenated through collective, irreversible rearrangements of atoms. Including additional static stress orientation in the loading protocol amplifies the rejuvenation effect, leading to improvements in the mechanical properties of metallic glasses.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2021)
Article
Materials Science, Multidisciplinary
Nikolai V. Priezjev
Summary: This study uses molecular dynamics simulations to investigate the effect of tensile stress applied during cooling of binary glasses on potential energy states and mechanical properties. The results show that higher applied stress can enhance potential energy and improve the plasticity of glasses. Additionally, the amorphous structure of rejuvenated glasses characterized by an increase in the number of contacts between smaller type atoms can enhance ductility in glasses prepared at larger applied stresses and higher initial temperatures.
Article
Materials Science, Ceramics
Nikolai V. Priezjev
Summary: The research revealed that the potential energy and mechanical properties of amorphous materials can be influenced by variable-amplitude loading. Proper loading can rejuvenate well-annealed glasses, while improper loading can lead to a gradual decrease in energy states of poorly annealed glasses.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2021)
Article
Materials Science, Ceramics
Nikolai V. Priezjev
Summary: This study investigates the effect of small-amplitude periodic shear on annealing of a shear band in binary glasses through molecular dynamics simulations. The results show that increasing strain amplitude leads to glasses being relocated to deeper potential energy levels, and mechanical tests demonstrate an increase in shear modulus and yield stress with loading at strain amplitudes close to the yield strain.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2021)
Article
Materials Science, Multidisciplinary
Nikolai V. Priezjev
Summary: The research found that with increasing glass stability, the shear modulus and yielding peak of periodically deformed binary glasses increase towards plateau levels, and the yielding transition occurs at higher amplitudes and becomes more abrupt. The initiation and formation processes of shear bands are elucidated through spatiotemporal analysis of nonaffine displacements.
COMPUTATIONAL MATERIALS SCIENCE
(2021)
Article
Clinical Neurology
Nikolai Priezjev, Francisco G. Vital-Lopez, Jaques Reifman
Summary: This study assessed the ability of biomathematical models to predict alertness impairment and found that these models have high accuracy in predicting alertness decline at both the group-average and individual levels. The results indicate that in three out of four psychomotor vigilance tests, it is difficult to distinguish between study data and model predictions.
JOURNAL OF SLEEP RESEARCH
(2023)
Article
Materials Science, Ceramics
Nikolai V. Priezjev
Summary: Molecular dynamics simulations were used to investigate the effect of cyclic shear deformation on structural relaxation and yielding in binary glasses. It was found that mechanical annealing occurred through intermittent plastic rearrangements, with the spatial extent decreasing as energy levels decreased. The yielding behavior was studied by adjusting strain amplitude, and it was observed that the critical strain amplitude remained constant regardless of the initial energy level. The formation of a shear band at the yielding transition was correlated with an increase in the number of atoms with large nonaffine displacements.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2022)
Article
Mechanics
Liuzhen Ren, Haibao Hu, Luyao Bao, Nikolai V. Priezjev, Jun Wen, Luo Xie
Summary: The study on the liquid-liquid interface at liquid-infused surfaces reveals different local slip modes under different viscosity ratios and elucidates the impact of viscosity ratio on effective slip length. The results may serve as a guide for optimizing the design of liquid-infused surfaces with enhanced slip properties.
Article
Materials Science, Ceramics
Pritam Kumar Jana, Nikolai Priezjev
Summary: The influence of cyclic loading and glass stability on structural relaxation and yielding transition in amorphous alloys was investigated using molecular dynamics simulations. It was found that rapidly cooled glasses under asymmetric cyclic shear gradually evolve towards states with lower potential energy and finite stress at zero strain. The yielding transition in more stable glasses can be delayed for hundreds of cycles when the strain amplitude is near a critical value.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2023)
Article
Materials Science, Multidisciplinary
Nikolai V. Priezjev
Summary: The study investigates the accumulation of plastic deformation and flow localization in amorphous alloys under periodic shear using molecular dynamics simulations. A well-annealed binary mixture of one million atoms subjected to oscillatory shear deformation with strain amplitudes slightly above a critical value is studied. The results show that the number of shear cycles until the yielding transition can be described by a power-law function when approaching a critical strain amplitude. The analysis of nonaffine displacements of atoms elucidates the process of strain localization, leading to the formation of a system-spanning shear band.
COMPUTATIONAL MATERIALS SCIENCE
(2023)
Article
Materials Science, Multidisciplinary
Nikolai V. Priezjev
Summary: This study investigates the effect of oscillatory shear deformation on fatigue life, yielding transition, and flow localization in metallic glasses using molecular dynamics simulations. The research reveals that at strain amplitudes below a critical value, plastic events are highly localized, while above the critical point, plastic deformation gradually accumulates until yielding transition and shear band formation across the system. Interestingly, when the strain amplitude approaches the critical value from above, the number of cycles to failure increases as a power-law function.
Meeting Abstract
Clinical Neurology
Jaques Reifman, Francisco Vital-Lopez, Nikolai Priezjev