Article
Physics, Multidisciplinary
Antonio Suma, Vincenzo Carnevale, Cristian Micheletti
Summary: Using theory and simulations, the authors studied DNA unzipping via nanopore translocation and found three dynamical regimes depending on the applied force. They showed that the normal regime can be modeled as a one-dimensional stochastic process and used the theory of stochastic processes to recover the free-energy landscape. This approach can be applied to other single-molecule systems with periodic potentials to obtain detailed free-energy landscapes from out-of-equilibrium trajectories.
PHYSICAL REVIEW LETTERS
(2023)
Article
Biochemical Research Methods
Lianjie Xue, Shiqiang Jin, Shinobu Nagasaka, Daniel A. Higgins, Takashi Ito
Summary: Fluorescence correlation spectroscopy (FCS) combined with maximum entropy method (MEM) allows for accurate measurement of molecular diffusion behavior in different samples. The study found that MEM-FCS can effectively analyze the number and average diffusion coefficients of multiple distinct diffusion modes, with greater advantage compared to other methods. Additionally, the validation of MEM-FCS results with single molecule tracking (SMT) data highlights the utility of MEM-FCS in obtaining information on molecular diffusion processes in materials.
JOURNAL OF FLUORESCENCE
(2022)
Article
Engineering, Chemical
Elijah Thimsen
Summary: This work elucidates methods based on nonequilibrium thermodynamics to predict the stationary states of chemical reactions in nonequilibrium plasma and the limits for energy conversion efficiency, using CO2 splitting as an example reaction. It was found that the probability of observing reactants or products increases with the energy dissipated by that side of the reaction as heat through collisions with hot electrons.
Article
Chemistry, Multidisciplinary
Xiang Zhu, Jiayu Xu, Yao Zhang, Bin Li, Yishu Tian, Yingying Wu, Zhiwei Liu, Chuanxu Ma, Shijing Tan, Bing Wang
Summary: Isotope substitution not only changes the vibrational frequencies but also the vibrational distributions in real-space of a molecule. Measuring isotope effects in a polyatomic molecule at the single-bond level with energy and spatial resolutions has been challenging. By achieving angstrom resolution in tip-enhanced Raman spectroscopy (TERS), the isotope effect of each vibrational mode in pentacene and its fully deuterated form is identified and measured. The frequency ratio ν(H)/ν(D) varies from 1.02 to 1.33, indicating different isotopic contributions of H/D atoms, which can be distinguished and described by TERS maps and potential energy distribution simulations. This study demonstrates that TERS can be a non-destructive and highly sensitive method for isotope detection and recognition with chemical-bond precision.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Mainak Dhar, Joseph A. Dickinson, Mark A. Berg
Summary: This study presents a nonparametric method for separating signal from noise using nonlinear-correlation functions. The method does not require a priori model, knowledge of system continuity or discreteness, fixed number of states, or knowledge of system Markovian property. The noise-corrected, nonlinear-correlation functions can be converted to system's Green's function and yield the system's equilibrium-probability distribution. Experimental results show that the proposed correlation method has better resolution in time and state space compared to other nonparametric approaches.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Brian T. O'Callahan, Patrick Z. El-Khoury
Summary: Tip-enhanced Raman spectroscopy is a powerful technique for high-resolution chemical imaging. It can track plasmon-induced/enhanced chemical reactions and provide accurate spectral assignments.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Johan Aqvist
Summary: Despite advances in computational design of protein structures, designing efficient enzyme catalysts remains challenging. This study uses extensive computer simulations to analyze the reasons for low catalytic activity and anomalous temperature behavior in a designed enzyme. The results reveal a lower energy state of the enzyme-substrate complex that explains the low activity and suggest two possible explanations for the temperature optimum: a change of rate-limiting step or a heat capacity change upon substrate binding.
Article
Optics
Raymundo Moya, Toru Kondo, Audrey C. Norris, Gabriela S. Schlau-Cohen
Summary: Single-molecule spectroscopy is widely used to study heterogeneity in behaviors on different timescales, with the recent emergence of single-molecule pump-probe spectroscopy for detecting heterogeneity on femtosecond and picosecond timescales. By developing a tunable apparatus, a bimodal distribution of energetic relaxation time constants was found for the fluorescent dye Atto647N, indicating dominance of specific processes within individual molecules and low heterogeneity. This spectrally-tunable single-molecule pump-probe spectroscopy has the potential to investigate heterogeneity in various biological and material systems.
Article
Chemistry, Multidisciplinary
Stefan Krause, Evelyn Ploetz, Johann Bohlen, Patrick Schuler, Renukka Yaadav, Florian Selbach, Florian Steiner, Izabela Kaminska, Philip Tinnefeld
Summary: Researchers screened 10 preparation methods for graphene-on-glass and presented an optimized protocol for single-molecule and super-resolution imaging; they utilized DNA origami technology to detect graphene quality, showing discrepancies between conventional techniques such as light microscopy, atomic force microscopy, and Raman spectroscopy for graphene characterization.
Article
Nanoscience & Nanotechnology
Abhay Kotnala, Hongru Ding, Yuebing Zheng
Summary: Plasmonic nanoapertures have various exciting applications, but traditional nanoapertures may result in weak light-matter interactions. A new hybrid nanoaperture design, AuNIs-e-NA, provides multiple electromagnetic hotspots and can achieve up to 4000-fold field enhancements, significantly improving fluorescence signals. With simple design, easy fabrication, and strong signal enhancements, AuNIs-e-NA is a robust platform for surface-enhanced optical sensing, imaging, and spectroscopy.
Review
Biochemistry & Molecular Biology
Rebeca Bocanegra, Ismael G. A. Plaza, Carlos R. Pulido, Borja Ibarra
Summary: The study reveals that the replisome machinery is stochastic, versatile, and highly dynamic, with transient protein-protein and protein-DNA interactions playing a key role in robust DNA replication.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Physical
Suraj Verma, Namasivayam Dhenadhayalan, King-Chuen Lin
Summary: The effect of gradual cholesterol increase on the dynamics of DOPC and DPPC membranes was investigated using single-molecule fluorescence correlation spectroscopy. The results showed that the rigidity of DOPC membranes increased with increasing cholesterol concentration, while the rigidity of DPPC membranes decreased.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
Prithu Roy, Jean-Benoit Claude, Sunny Tiwari, Aleksandr Barulin, Jerome Wenger
Summary: The study demonstrates the use of ultraviolet autofluorescence of tryptophan amino acids to study single proteins without fluorescence labeling. By combining nanophotonic plasmonic antennas, antioxidants, and background reduction techniques, the sensitivity of label-free ultraviolet fluorescence correlation spectroscopy (UV-FCS) is improved to the level of single tryptophan residues. This breakthrough enables the application of UV-FCS to a wide range of label-free proteins.
Article
Chemistry, Multidisciplinary
Lukas Whaley-Mayda, Abhirup Guha, Samuel B. Penwell, Andrei Tokmakoff
Summary: The combination of infrared-vibrational absorption and fluorescent electronic transition techniques in FEIR spectroscopy enables single-molecule sensitivity in solution, allowing for measurement of vibrational spectra and relaxation processes. Introduction of FEIR correlation spectroscopy demonstrates the potential for single-molecule sensitivity in vibrational investigations in solution or condensed phase.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Damir Sakhapov, Ingo Gregor, Narain Karedla, Joerg Enderlein
Summary: We propose a new method that combines fluorescence correlation spectroscopy (FCS) on the microsecond time scale with fluorescence antibunching measurements on the nanosecond time scale for measuring photophysical rate constants of fluorescent molecules. The method allows for accurate measurement of photophysical rate constants of different dyes through theoretical analysis and experiment.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)