Review
Chemistry, Multidisciplinary
Haonan Chang, Jun Zhang
Summary: This review discusses the mechanisms of cavity optomechanical coupling, the principles of exciton optomechanical coupling, and the recent progress in cavity-less exciton optomechanics. The integration potential of cavity-less exciton optomechanical systems is highlighted, along with their highly tunable exciton resonance.
Article
Optics
A. N. Ikot, U. S. Okorie, I. B. Okon, L. F. Obagboye, A. Ahmadov, H. Y. Abdullah, K. W. Qadir, M. E. Udoh, C. A. Onate
Summary: In this study, the analytical solutions of the 2D Schrodinger equation for a new Morse interacting potential were comprehensively investigated. The thermodynamic and thermomagnetic properties of the system were analyzed and it was found that temperature and maximum quantum number have significant effects on the properties of the system.
EUROPEAN PHYSICAL JOURNAL D
(2022)
Review
Chemistry, Physical
T. Gil-Diaz, D. Jara-Heredia, F. Heberling, J. Luetzenkirchen, J. Link, T. Sowoidnich, H-M Ludwig, M. Haist, T. Schaefer
Summary: This study presents a method of quantifying particle-particle interactions through charge regulation, considering changes in solution and surface speciation upon particle approach. By coupling surface complexation models with the Poisson-Boltzmann equation, the accuracy of inter-particle force calculations is greatly improved. The flexibility and precision of the approach are demonstrated through benchmark calculations, showing potential applications in various industrial, biological, and environmental systems.
ADVANCES IN COLLOID AND INTERFACE SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Ankit Kumar Singh, Zhan-Hong Lin, Min Jiang, Thomas G. G. Mayerhoefer, Jer-Shing Huang
Summary: Chiral molecules exhibit differences in chemical and optical properties due to different spatial arrangements. Optical differentiation is commonly achieved through detection of absorption circular dichroism (CD). However, CD in typical molecules is limited by its small magnitude. Cavity ring-down spectroscopy (CRDS) is an ultrasensitive absorption spectroscopic method for low-absorbing gas-phase samples. In this study, we propose a metasurface-assisted EW-CRDS platform for ultrasensitive chiral absorption spectroscopy, enabling CD detection with linearly polarized light. The findings open up possibilities for highly-sensitive thin film detection of chiral molecules using CRDS techniques.
Article
Chemistry, Physical
Yogita Silori, Sakshi Chawla, Anita Yadav, Arijit K. De
Summary: This study investigates the ultrafast singlet fission dynamics of triisopropylsilylethynyl pentacene in micellar nanocavities. The results show that smaller nanoparticles exhibit higher singlet fission efficiency compared to larger nanoparticles.
Article
Chemistry, Physical
Desiree A. Rehel, James M. Polson
Summary: Experiments using nanofluidic devices have been effective in studying the physical properties of confined polymers in small cavities. Two recent studies focused on the organization and dynamics of DNA molecules in box-like cavities with different cross-sectional shapes. Inspired by these experiments, Monte Carlo and Brownian dynamics simulations were used to investigate the behavior of polymers confined in similar-shaped cavities. Various polymer properties and confinement dimensions were varied, revealing that polymer width, cavity elongation, and contour length difference significantly impact polymer organization and dynamics.
Article
Biology
Jia Yi Kimberly Low, Xiangyan Shi, Venkatraman Anandalakshmi, Dawn Neo, Gary Swee Lim Peh, Siew Kwan Koh, Lei Zhou, M. K. Abdul Rahim, Ketti Boo, JiaXuan Lee, Harini Mohanram, Reema Alag, Yuguang Mu, Jodhbir S. Mehta, Konstantin Pervushin
Summary: ATP-independent amyloid-beta chaperone L-PGDS can disaggregate corneal amyloids in surgically excised human cornea of TGFBI-related corneal dystrophy patients by recognizing and releasing structurally frustrated regions. This mechanism provides insights into the alternative source of energy utilized by ATP-independent disaggregases and highlights the possibility of using these chaperones as treatment strategies for different types of amyloid-related diseases.
COMMUNICATIONS BIOLOGY
(2023)
Article
Physics, Applied
Naoki Azuma, Kenji Fukuzawa, Shintaro Itoh
Summary: This study focused on stretching and immobilizing lambda DNA molecules in a microchannel to achieve super-resolution imaging using dSTORM. By controlling pressure in the microchannel and utilizing YOYO-1 dye blinking, they successfully obtained super-resolution imaging with a half maximum width of 67 nm. Improving the design of the microchannel is essential for enhancing dSTORM imaging of DNA molecules in future studies.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Nana Ma, Keman Cheng, Qingqing Feng, Guangna Liu, Jie Liang, Xiaotu Ma, Zhiqiang Chen, Yichao Lu, Xinwei Wang, Wei He, Hu Xu, Shan Wu, Jiajia Zou, Quanwei Shi, Guangjun Nie, Xiao Zhao
Summary: In this study, a flat rectangular DNA origami is used as a display scaffold and a strategy called engraving-printing is developed to rapidly decorate three TRAIL monomers onto its surface to form DNA-TRAIL3 trimers. By comparing the receptor affinity, agonistic activity, and cytotoxicity, it is found that the critical interligand distance of DNA-TRAIL3 trimers to induce death receptor clustering and resulting apoptosis is approximately 40 nm.
Article
Polymer Science
Ye Chen, Xiaofei Tian, Xiaolei Xu, Wen-Sheng Xu, Jizhong Chen
Summary: In this study, the search process of monomers of a Rouse chain confined in a spherical cavity with a small opening was investigated using scaling analysis and Langevin dynamics simulations. It was found that the search process is Markovian when the radius of gyration is smaller than the cavity radius, but becomes non-Markovian when it is larger. The study also revealed that the subdiffusion of monomers under confinement depends on their positions in the chain.
Article
Optics
Michal Smialkowski, Michal Tomza
Summary: The properties of highly polar diatomic molecules containing S-2-state transition-metal atoms were theoretically investigated. Various molecular properties such as potential energy curves, permanent electric dipole moments, spectroscopic constants, and leading long-range dispersion-interaction coefficients were calculated. The studied molecules exhibit strongly bound covalent or ionic bonds in the ground electronic state, resulting in very large permanent electric dipole moments.
Article
Physics, Fluids & Plasmas
Jialu Chen, Liang Sun, Simin Wang, Fujia Tian, Haoqi Zhu, Ruiqin Zhang, Liang Dai
Summary: This work reports an intriguing phenomenon of crowding-induced polymer trapping in channels, where crowding particles push the polymer into channel corners through an effective polymer-corner attraction. The occurrence of polymer trapping depends on the minimum volume fraction of crowders, which scales with crowder and monomer diameters. The nearly fully stretched polymer conformation resulting from polymer trapping may have practical applications, such as in nanochannel-based genome mapping technologies.
Article
Chemistry, Multidisciplinary
Qufei Gu, Huan H. Cao, Yehan Zhang, Haiyang Wang, Zachary J. Petrek, Fukun Shi, Eric A. Josephs, Tao Ye
Summary: By analyzing spatial statistical data and developing a phenomenological model, we investigated how the hybridization rates of probe molecules in surface environments are influenced, revealing the significant role of nanoscale spatial organization in hybridization kinetics. This study provides valuable insights for the development of more sensitive and reproducible DNA biosensors and microarrays.
Article
Chemistry, Physical
Peter Cifra, Tomas Bleha
Summary: Simulation study reveals that the pressure of polymers increases with chain stiffness but is not affected by chain topology in a closed cavity. For flexible polymers, the computed pressure dependence on cavity size and polymer concentration is consistent with the expected scaling behavior. However, the scaling behavior of semiflexible polymers only partially agrees with the theory prediction due to the continuous transition between regimes for chains of moderate lengths. The computed segment density profiles support the tendency of semiflexible polymers to concentrate beneath the cavity surface and elevate the pressure. The compaction of polymers into disordered globules or growing toroidal structures is demonstrated.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Youngkyun Jung, Bae-Yeun Ha
Summary: This study investigates the compaction transition of heterogeneous polymers with ring topology under crowding effects using molecular dynamics simulations. The results reveal a two-step process of compaction and suggest that cylindrical confinement enhances the initial compaction, supporting the idea that crowding promotes clustering of active transcription units into transcription factories.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Polymer Science
Yue Qi, Lili Zeng, Ahmed Khorshid, Reghan J. Hill, Walter W. Reisner
Article
Multidisciplinary Sciences
Susan Amin, Ahmed Khorshid, Lili Zeng, Philip Zimny, Walter Reisner
NATURE COMMUNICATIONS
(2018)
Article
Multidisciplinary Sciences
Nicolas Soubry, Andrea Wang, Rodrigo Reyes-Lamothe
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Review
Microbiology
Rodrigo Reyes-Lamothe, David J. Sherratt
NATURE REVIEWS MICROBIOLOGY
(2019)
Review
Biochemistry & Molecular Biology
Nitin Kapadia, Rodrigo Reyes-Lamothe
BIOCHEMICAL SOCIETY TRANSACTIONS
(2019)
Article
Multidisciplinary Sciences
Anne-Marie Ladouceur, Baljyot Singh Parmar, Stefan Biedzinski, James Wall, S. Graydon Tope, David Cohn, Albright Kim, Nicolas Soubry, Rodrigo Reyes-Lamothe, Stephanie C. Weber
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Nitin Kapadia, Ziad W. El-Hajj, Rodrigo Reyes-Lamothe
Summary: DNA-bound proteins play essential roles in genome maintenance and regulation, and the machine learning approach Bound2Learn can accurately estimate the residence times of protein-DNA interactions, facilitating the understanding of biological processes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Imman I. Hosseini, Zezhou Liu, Xavier Capaldi, Tamer AbdelFatah, Laura Montermini, Janusz Rak, Walter Reisner, Sara Mahshid
Summary: Extracellular vesicles (EVs) are cell-derived membrane structures circulating in body fluids, showing potential for noninvasive diagnosis. To fully utilize the diagnostic potential of EVs, technologies that can analyze large populations of EVs without sacrificing single EV detail are needed.
Review
Medicine, General & Internal
Ze-Hua Lai, Kai-Qi Ding, Xuan-Qiang Tu, Yuan-Yue Song, Li-Li Zeng
Summary: This article reports the first case of idiopathic hypereosinophilic syndrome presenting as ischemic cerebrovascular disease and capsular warning syndrome. Adequate glucocorticoid and anticoagulant treatments resulted in symptom improvement.
Article
Chemistry, Physical
Zezhou Liu, Sarah M. Christensen, Xavier Capaldi, Seyed Imman Hosseini, Lili Zeng, Yuning Zhang, Rodrigo Reyes-Lamothe, Walter Reisner
Summary: Bacteria have various large dsDNA molecules that interact within the cell and are affected by cell morphology, leading to non-uniform spatial organization and dynamics. This study investigates how plasmid copy number and confinement geometry affect plasmid distribution and dynamics using an in vitro nanofluidic model. The results show that increased plasmid number changes distribution and reduces polar dwell time, while sharper cavity end curvature leads to longer dwell time.
Article
Physics, Fluids & Plasmas
Lili Zeng, Walter W. Reisner
Summary: In this study, molecular dynamics simulation was used to investigate the nonequilibrium physics of single nanochannel-confined semiflexible polymers in a homogeneous flow field. The results showed that the flow-based compression of the polymer against the end of the nanochannel led to a distinct organization of folds and circular coils. The organization varied with the stiffness of the chains and the flow speed, but was ultimately determined by the minimization of the total chain free energy.
Article
Physics, Fluids & Plasmas
Ingrid Gendron, Katherine Savard, Xavier Capaldi, Zezhou Liu, Lili Zeng, Walter Reisner, Luc Capaldi
Summary: Experimental setup allows for confined macro-scale knot formation through tumbling, enabling research on knotting probability, complexity, and dynamics, revealing saturation in knot formation below a critical length and indication of nonequilibrium conditions. Longer chains tend to form knots of higher complexity due to increased access to loops during tumbling despite saturation in knot formation.