Article
Chemistry, Physical
Fei Zhang, Xikai Jiang, Gaofeng Chen, Yadong He, Guoqing Hu, Rui Qiao
Summary: This study investigated the electric-field-driven ion emission from the free surface of an RTIL film using molecular dynamics simulations. It found that the rate and composition of ion emission are determined by the external field and ion-surface interactions. The results provide fundamental insights to improve ion evaporation theories and enhance the performance of electrospray applications.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Analytical
Zhumei Rohskopf, Taehong Kwon, Sung Hee Ko, Dragana Bozinovski, Hyungkook Jeon, Naresh Mohan, Stacy L. Springs, Jongyoon Han
Summary: This study developed a novel nanofluidic system for continuous direct measurement of IgG titers, enabling online monitoring and showing good correlation with biolayer interferometry assays.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Tomas F. D. Silva, Diogo Vila-Vicosa, Miguel Machuqueiro
Summary: This study utilized a new pH-replica exchange method to simulate pHLIP in membranes of varying sizes, revealing that conformational heterogeneity due to strong electrostatic interactions was the primary source of pK(a) variability. Despite challenges, deeper pK(a) values still accurately predicted experimental insertion pK. Additionally, the use of large membrane patches was necessary for stable and realistic pHLIP/membrane systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Tetsuya Morishita
Summary: The time-dependent PCA method incorporating time dependence can clearly identify structural changes and collective fluctuations, playing an important role in provoking structural transformations and enhancing sampling in MD simulations.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Mitra Lal, Ellen Wachtel, Mordechai Sheves, Guy Patchornik
Summary: This study demonstrates the use of physical chemistry to direct protein binding to non-ionic detergent micelles, allowing for controlled aggregation and deaggregation of micelles, providing greater flexibility in membrane protein purification and crystallization processes.
Article
Biochemistry & Molecular Biology
Farindra Kumar Mahto, Akash Bhattacharya, Swati Bhattacharya
Summary: The Hsp70 chaperone protein system is crucial for protein folding and homeostasis. Molecular dynamics simulations reveal that the Lid domain has greater conformational flexibility than previously expected.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Physics, Multidisciplinary
Nicola Molinari, Yu Xie, Ian Leifer, Aris Marcolongo, Mordechai Kornbluth, Boris Kozinsky
Summary: The method uses spectral decomposition of short-time ionic displacement covariance to accelerate computations of ionic conductivity and reduce uncertainty. It demonstrates robustness through mathematical and numerical proofs, and is applied to realistic electrolyte materials.
PHYSICAL REVIEW LETTERS
(2021)
Article
Food Science & Technology
Kevion K. Darmawan, Tom C. Karagiannis, Jeff G. Hughes, Darryl M. Small, Andrew Hung
Summary: Research demonstrates a stable interaction between the cell wall component of lactic acid bacteria and a protein complex, consisting of milk proteins, with stronger hydrophobic interactions at higher spray drying temperatures. This indicates the potential for developing novel nutraceuticals with enhanced antibacterial properties.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Thomas J. Oweida, Yaroslava G. Yingling
Summary: This study presents a method that integrates experimental small-angle X-ray scattering data and all-atom molecular modeling data using a genetic algorithm method for the determination of the atomistic representation of poly-Thymine DNA in solution. The results validate the performance of various AMBER force fields and implicit solvent models for ssDNA and enable a better understanding of the behavior of ssDNA in solution.
ADVANCED THEORY AND SIMULATIONS
(2023)
Article
Biology
Aayush Gupta, Souvik Dey, Alan Hicks, Huan-Xiang Zhou
Summary: This study developed generative autoencoders that can learn from short molecular dynamics simulations and generate full conformational ensembles of intrinsically disordered proteins.
COMMUNICATIONS BIOLOGY
(2022)
Article
Physics, Multidisciplinary
Tine Curk, Erik Luijten
Summary: Nanoparticles in solution acquire charge through surface groups, requiring the use of charge-regulating boundary conditions for proper description of electrostatic interactions. A hybrid Monte Carlo/molecular dynamics scheme is implemented to dynamically adjust charges of surface groups, qualitatively changing self-assembled structures. The conventional constant-charge approximation may be used under certain conditions, and the interplay between charge regulation and dielectric polarization is clarified.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Pablo Martinez-Crespo, Martin Otero-Lema, Oscar Cabeza, Hadrian Montes-Campos, Luis M. Varela
Summary: In this study, classical Molecular Dynamics and ab initio Density Functional Theory simulations were used to investigate the structure and single particle dynamics of ternary mixtures. The coordination numbers and electrical conductivities of different mixtures were calculated, and the differences between mixtures with protic and aprotic ionic liquids were analyzed, along with solvation and charge transport mechanisms.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
Changxiong Huang, Zhen Li, Xiaohong Zhu, Na Li, Xinyao Ma, Jun Fan
Summary: Solid-state nanopore sequencing faces problems of pore clogging and fast speed, and this study proposes nanoslit sensing based on the planar heterostructure of graphene and hexagonal boron nitride. Molecular dynamics simulations show that DNA molecules are confined within the heterostructure and can permeate through nanoslits in two ways. This study sheds light on the sensing mechanism and provides theoretical guidance on designing devices controlling molecular transportation.
Article
Chemistry, Multidisciplinary
Robert M. Ziolek, Alejandro Santana-Bonilla, Raquel Lopez-Rios de Castro, Reimer Kuhn, Mark Green, Christian D. Lorenz
Summary: In this study, the nanoscale structure of the polymer F8BT and its impact on its optical properties were investigated using molecular dynamics simulations. The researchers found a giant percolating cluster in amorphous F8BT, which has implications for the quantum yield and color shift observed in conjugated polymer-based devices and nanostructures. Additionally, the study showed that distinct conformations can be unraveled from the disordered structure of amorphous F8BT using a machine learning protocol.
Article
Chemistry, Applied
Kevion K. Darmawan, Tom C. Karagiannis, Jeff G. Hughes, Darryl M. Small, Andrew Hung
Summary: This study investigates the structural changes of apo-LF and its interactions with alpha-La and beta-Lg at low temperatures through computational methods. Results show that alpha-La and beta-Lg stabilize apo-LF by enhancing and maintaining its structural integrity, forming a multimeric complex. The secondary structure and anti-bacterial derivatives of apo-LF are sustained under simulated conditions, and interresidue contact maps predict an increase in intramolecular contacts during freeze-drying, potentially affecting protein dispersibility during rehydration.
FOOD HYDROCOLLOIDS
(2021)