Article
Chemistry, Multidisciplinary
Edyta M. Greer, Victor Siev, Ayelet Segal, Alexander Greer, Charles Doubleday
Summary: This study presents the first computation of multidimensional tunneling in a reaction sequence, showing that quantum tunneling has significant contributions to the rate constants. In the steps of Diels-Alder reaction and keto-enol tautomerization, tunneling effects create shallow energy minima. Predicted kinetic isotope effects can be observed experimentally.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Jing Sun, Oriol Vendrell
Summary: The modification of thermal chemical rates in Fabry-Perot cavities presents challenges in theoretical understanding. This study investigates the effect of activated and nonactivated molecules on the reaction rates of gas-phase HONO molecules. It is found that nonactivated molecules enhance energy dissipation, while activated molecules couple with the resonances created by nonactivated molecules and the cavity, resulting in accelerated rates.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biophysics
Matthew J. Satusky, Caitlin V. Johnson, Dorothy A. Erie
Summary: We have developed an easy, inexpensive, and sequence-independent method for site-specific labeling of DNA oligonucleotides. By utilizing commercially synthesized oligonucleotides containing phosphorothioate diester(s) and a bifunctional linker, we were able to label the DNA and demonstrate its effectiveness through fluorescence resonance energy transfer and biochemical activity assays. This technology offers a cost-effective alternative to current labeling methods and provides opportunities for unrestricted exploration in DNA research.
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Matthew R. Adendorff, Guo Qing Tang, David P. Millar, Mark Bathe, William P. Bricker
Summary: In this study, molecular dynamics simulations were used to investigate the base-pair level structure and dynamics of four-way junctions, revealing the significant impact of base sequence on local structure, isomer bias, and global junction dynamics.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Physical
Luchun Lin, Chun Tang, Gang Dong, Zhixin Chen, Zhichao Pan, Junyang Liu, Yang Yang, Jia Shi, Rongrong Ji, Wenjing Hong
Summary: The single-molecule break junction technique allows for exploring charge transport phenomena at the ultimate scale of a single molecule, but traditional data analysis methods may overlook important conductance variations. A customized spectral clustering method combined with the evaluation of the Calinski-Harabasz index has been demonstrated to be suitable for analyzing large datasets and automatically extracting different molecular junction conformations, offering a promising algorithm for junction conformation analysis in massive break junction data.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Biochemistry & Molecular Biology
Keisuke Ikawa, Shuji Ishihara, Yoichiro Tamori, Kaoru Sugimura
Summary: Epithelial cells undergo cell rearrangement by remodeling cell adhesion and changing their neighbors to shape a tissue. This process involves junction shrinkage, exchange, and elongation, which are facilitated by the formation of myosin-II cables around cell vertices. The detachment of myosin-II from the cell cortex is regulated by the proteins Jub and M6. The interplay between Jub and M6, dependent on junction length, orchestrates the detachment of myosin-II cables and the shrinkage/elongation of junctions during cell rearrangement. A mechanical model based on wetting theory explains how the physical properties of myosin-II cables and junction geometry contribute to the exchange of junctions in a unidirectional manner.
Article
Physics, Multidisciplinary
Christopher L. Smallwood, Ronald Ulbricht, Matthew W. Day, Tim Schroeder, Kelsey M. Bates, Travis M. Autry, Geoffrey Diederich, Edward Bielejec, Mark E. Siemens, Steven T. Cundiff
Summary: A high-density sample of negatively charged silicon-vacancy (SiV-) centers in diamond was characterized using collinear optical multidimensional coherent spectroscopy, revealing a hidden population of SiV- centers with significant spectral inhomogeneity and extended electronic T-2 times, likely caused by strain and providing a potential mechanism for controlling electric coherence in color-center-based quantum devices.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Hanui Kim, Jong Goo Kim, Tae Wu Kim, Sang Jin Lee, Shunsuke Nozawa, Shin-ichi Adachi, Kihwan Yoon, Joonghan Kim, Hyotcherl Ihee
Summary: Extensive studies have been conducted on the isomer species formed by photodissociation of haloalkanes in solution. However, the molecular structure of the precursor of the isomer and its in-cage isomerization mechanism remain elusive. The structural dynamics of CH2I2 upon 267 nm photoexcitation in methanol were probed with femtosecond X-ray solution scattering, revealing unusual characteristics consistent with either a vibrationally hot form of the CH2I-I isomer or the loosely-bound radical pair.
Article
Mathematics, Interdisciplinary Applications
Marcell Stippinger, Balint Varga, Zsigmond Benko, Daniel Fabo, Lorand Eross, Zoltan Somogyvari, Andras Telcs
Summary: This article introduces a method for causal discovery based on temporal observations, which overcomes the limitations of limited data and hidden common drivers in causal relationships among dynamical systems exhibiting chaotic attractors. By measuring the complexity of rank order patterns in the embedded series, the method can effectively detect unidirectional and bidirectional causation, as well as hidden common causes. To validate its performance, the method is applied to synthetic datasets and human electrophysiological data, providing insights into the involvement of the left and right hippocampus before, during, and after epileptic seizures.
CHAOS SOLITONS & FRACTALS
(2023)
Article
Physics, Fluids & Plasmas
A. Chacoma, O. Billoni, M. N. Kuperman
Summary: In this article, the dynamics of marking in football matches are studied by analyzing the trajectories of players on the field. A temporal bipartite network of proximity is constructed to describe the dynamics. The study reveals a scaling law for the heterogeneity parameter of the networks, indicating the emergence of complexity in the system. Additionally, a simple model is proposed to simulate the players' motion and it proves to be useful in elucidating the underlying mechanisms responsible for the observed phenomena.
Article
Computer Science, Software Engineering
Sadashige Ishida, Chris Wojtan, Albert Chern
Summary: This paper presents a new method for representing curve dynamics, which uses an implicit description of curves to improve numerical stability and handle topological changes and re-connection events.
ACM TRANSACTIONS ON GRAPHICS
(2022)
Article
Physics, Multidisciplinary
Florian Otterpohl, Peter Nalbach, Michael Thorwart
Summary: In this study, we investigate the dynamics of a quantum two-level system immersed in a sub-Ohmic bath. By numerical simulations, we find that the system exhibits aperiodic behavior in the strong coupling regime.
PHYSICAL REVIEW LETTERS
(2022)
Article
Chemistry, Physical
Dehui Qiu, Mingpan Cheng, Petr Stadlbauer, Jielin Chen, Michal Langer, Xiaobo Zhang, Qiang Gao, Huangxian Ju, Jiri Sponer, Jean-Louis Mergny, David Monchaud, Jun Zhou
Summary: The active sites of natural and artificial enzymes play a crucial role in their catalytic performance. This study focuses on G-quadruplex (GQ)/hemin DNAzymes and investigates how their active sites can be controlled and manipulated. Experimental and molecular dynamics simulation results reveal that the topology of the GQ and the flanking nucleotides influence the activation of hemin, providing valuable insights into the biocatalytic activity of GQs.
Article
Physics, Multidisciplinary
Dominic J. Skinner, Boya Song, Hannah Jeckel, Eric Jelli, Knut Drescher, Joern Dunkel
Summary: Recent advances in microscopy techniques allow for studying complex biophysical systems at single-cell resolution, distinguishing structurally different cellular materials through a topological earth mover's (TEM) distance, and revealing a topological optimal transport problem in fruit fly wing development.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Amira Elbakry, Szilvia Juhasz, Ki Choi Chan, Markus Loebrich
Summary: Homologous recombination (HR) is a crucial DNA repair pathway that involves copying lost sequence information from an undamaged template to repair double-strand breaks (DSBs). ATRX-dependent HR outcompetes SDSA for the repair of most two-ended DSBs and leads to frequent CO formation. The choice of subpathway depends on the interaction of ATRX and RECQ5 with proliferating cell nuclear antigen.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Yonghyun Song, Changbong Hyeon
Summary: This study reviews the trade-offs between speed, fluctuations, and thermodynamic cost in biological processes and discusses the optimization in nonequilibrium states. It finds suboptimal precision of enzymatic processes at a given thermodynamic cost, with key biological processes working around this condition. The research delves into how biological systems evolve through optimization and balancing conflicting functional requirements.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemical Research Methods
Ji Hyun Bak, Min Hyeok Kim, Lei Liu, Changbong Hyeon
Summary: This study develops a unified framework for modeling and inferring chromatin domain structures over multiple scales, offering a quantitative view of multi-scale chromatin organization and revealing its connections with genome function.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Anvy Moly Tom, Won Kyu Kim, Changbong Hyeon
Summary: The study investigates the impact of mobile polymer brushes on proteins embedded in biological membranes using theoretical models and simulations. The depletion attraction between proteins due to brush polymers changes non-monotonically with the size of the brush; the interaction increases linearly with brush size as long as the brush height is shorter than the protein size. However, when the brush height exceeds the protein size, the depletion attraction among proteins is slightly reduced.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Pureun Kim, Changbong Hyeon
Summary: Temporal order in living matters reflects the self-organizing nature of dynamical processes driven out of thermodynamic equilibrium. The precision of biochemical oscillations is constrained by the thermodynamic cost according to the thermodynamic uncertainty relation (TUR). Glycolytic oscillations under cellular conditions are found to be cost-effective, with minimal entropy production when the oscillation period is between 5-10 minutes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Multidisciplinary Sciences
Changwon Kim, Min Ju Shon, Sung Hyun Kim, Gee Sung Eun, Je-Kyung Ryu, Changbong Hyeon, Reinhard Jahn, Tae-Young Yoon
Summary: Using single-molecule methods, researchers demonstrated the cooperativity between NSF and the SNARE complex to prevent ATP consumption without productive disassembly.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Yonghyun Song, Changbong Hyeon
Summary: Spatial boundaries in animal development are formed by prepatterning of tissues by signaling molecules called morphogens. The accuracy of boundary location is limited by fluctuations in morphogen concentration, which control the expression level of target genes. Producing more morphogen molecules to reduce fluctuations can lead to more precise target boundaries, but also incurs higher thermodynamic cost. In order to achieve a precise morphogen profile with minimal cost, the characteristic length of the concentration profile should be roughly half the distance to the target boundary position from the source.
Biographical-Item
Chemistry, Physical
Margaret S. Cheung, Ruxandra I. Dima, Changbong Hyeon
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemical Research Methods
Lei Liu, Bokai Zhang, Changbong Hyeon
Summary: The study highlights the importance of multi-way chromatin contacts in gene regulation, proposing a method to predict these contacts from Hi-C data. By analyzing pairwise genomic contact frequencies, the study reveals correlations and insights into related issues, such as cell-line dependent assemblies of genes and enhancers to chromatin hubs.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biophysics
Seonghoon Kim, Changbong Hyeon
Summary: This study used molecular dynamics simulations to investigate the positioning of TEMPO spin label in lipid bilayers. The results showed that the location of TEMPO is dependent on the membrane phase, with it being stabilized above the interface in the gel phase and below the interface in the fluid phase. This finding highlights the importance of assessing lipid packing order and fluidity under specific measurement conditions.
BIOPHYSICAL JOURNAL
(2022)
Article
Biophysics
Lei Liu, Xinmeng Cao, Bokai Zhang, Changbong Hyeon
Summary: Genome architecture mapping (GAM) is a method to probe and decipher three-dimensional chromatin organization. It provides the cosegregation probability of two genomic segments from nuclear profiles. However, the cosegregation probability is different from the contact probability and has a weaker correlation with interlocus distance. The study suggests that a properly normalized version of cosegregation probability calculated from a large number of nuclear slices is needed to achieve a strong correlation with interlocus distance.
BIOPHYSICAL JOURNAL
(2022)
Article
Computer Science, Interdisciplinary Applications
Kiri Choi, Won Kyu Kim, Changbong Hyeon
Summary: This study proposes a systematic and principled method for classifying neurons based on the idea of polymer physics. By calculating the 3D coordinates of neurons and analyzing the resulting distance distribution, the authors are able to quantitatively characterize the morphology of neurons and classify them based on their structural similarities. This method provides valuable insights into the dense neural networks in the brain.
Article
Biology
Kiri Choi, Won Kyu Kim, Changbong Hyeon
Summary: Reconstructed from electron microscope images, the projection neurons of the Drosophila olfactory system provide a detailed view of neuronal anatomy and shed light on the relationship between neuronal organization and odor perception.
Article
Chemistry, Physical
Lei Liu, Changbong Hyeon
Summary: Confined polymer chains in two-dimensional planes are segregated due to topological interaction. The properties of the solution depend on the solvent quality, and the osmotic pressure increases with the area fraction, with different rates for good and bad solvents. Numerical simulations show that polymer chains in bad solvents occupy the surface in a more inhomogeneous manner and have a greater correlation length, leading to a higher and more heterogeneous interstitial void size.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Meeting Abstract
Biophysics
Seonghoon Kim, Changbong Hyeon
BIOPHYSICAL JOURNAL
(2022)
Article
Physics, Fluids & Plasmas
Davinder Singh, Changbong Hyeon
Summary: This study investigates the characteristics of thermodynamic uncertainty relations (TURs) in open quantum systems, revealing that the imaginary part of quantum coherence leads to a relaxation of the TUR bound, while the real part of coherence tightens it.