Article
Multidisciplinary Sciences
Cesar Diaz-Celis, Cristhian Canari-Chumpitaz, Robert P. Sosa, Juan P. Castillo, Meng Zhang, Enze Cheng, Andy Q. Chen, Michael Vien, Jeong Hoon Kim, Bibiana Onoa, Carlos Bustamante
Summary: DNA unwrapping and disassembly of nucleosomes play a crucial role in genomic access and transcription regulation. This study, using high-resolution optical tweezers and single-molecule FRET detection, reveals the asymmetry in nucleosome unwrapping and identifies the DNA segments involved in the process. It also suggests the stochastic disassembly of nucleosomes into hexasomes and tetrasomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Hisashi Ishida, Hidetoshi Kono
Summary: Torsional stress significantly influences the stability of the nucleosome by impacting the unwrapping of DNA. Positive stress leads to large-scale asymmetric unwrapping, while negative stress increases DNA flexibility for stable binding. The torsional stress alters the affinity of DNA and the octamer, affecting the accessibility of regulatory proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Soon-Keat Ooi, Shigeo Sato, Chieri Tomomori-Sato, Ying Zhang, Zhihui Wen, Charles A. S. Banks, Michael P. Washburn, Jay R. Unruh, Laurence Florens, Ronald C. Conaway, Joan W. Conaway
Summary: PARP1 has multiple functions in ALC1-dependent nucleosome remodeling beyond simply synthesizing PAR chains, as shown by investigation of separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Xinqiang Ding, Xingcheng Lin, Bin Zhang
Summary: The study utilized a near-atomistic model to investigate the structure and dynamics of chromatin, revealing multiple pathways connecting chromatin configurations and influencing the in situ relevance of the 30 nm fiber.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Havell Markus, Jun Zhao, Tania Contente-Cuomo, Michelle D. Stephens, Elizabeth Raupach, Ahuva Odenheimer-Bergman, Sydney Connor, Bradon R. McDonald, Bethine Moore, Elizabeth Hutchins, Marissa McGilvrey, Michelina C. de la Maza, Kendall Van Keuren-Jensen, Patrick Pirrotte, Ajay Goel, Carlos Becerra, Daniel D. Von Hoff, Scott A. Celinski, Pooja Hingorani, Muhammed Murtaza
Summary: Urinary cfDNA fragments exhibit specific patterns of fragmentation, suggesting temporary protection and robustness against preanalytical perturbations. The genome-wide sequencing coverage revealed protected regions conserved across individuals, with potential implications for cancer diagnostics. Furthermore, the fragmentation patterns of urine cfDNA show correlations with gene expression and chromatin accessibility in epithelial cells of the urinary tract, indicating their potential use in cancer diagnostics.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Materials Science, Multidisciplinary
Kaili Jiang, Michele Pavanello
Summary: Time-dependent orbital-free density functional theory is an efficient method for calculating dynamic properties of large-scale quantum systems. The method involves mapping the real system of interacting fermions onto a fictitious system of noninteracting bosons, with key ingredients being the dynamic Pauli potential and associated kernel. The proposed frequency-dependent Pauli kernel shows promising results for improving the accuracy of orbital-free DFT simulations for nanoscale systems.
Article
Optics
Huan Cui, Jie Cao, Qun Hao, Dong Zhou, Mingyuan Tang, Kaiyu Zhang, Yingqiang Zhang
Summary: The research proposes an omnidirectional ghost imaging system that can achieve a 360 degrees omnidirectional field of view with the addition of a curved mirror, obtaining undistorted and unwrapping-free panoramic images with uniform resolution.
Article
Biochemistry & Molecular Biology
Hisashi Ishida, Hidetoshi Kono
Summary: Nucleosome reconstitution is crucial for cellular functions, and the displacement of the H2A-H2B dimer is a key step. In this study, adaptive biased molecular dynamics and umbrella sampling simulations were used to investigate the free energy landscape of the dimer displacement. The docking domain of H2A and the C-terminal of H4 were identified as the main contributors to the free energy. The extent of nucleosomal DNA wrapping determined the different paths for the dimer displacement, suggesting that external factors such as histone chaperones can modulate the displacement path. Additionally, key residues involved in the free energy were found to be related to nucleosome assembly, reassembly, and posttranslational modifications (PTMs) in cancer cells.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Peter R. Eriksson, David J. Clark
Summary: Research reveals that ISW1b primarily regulates nucleosome spacing and resolution of closely packed dinucleosomes, with ISW1a playing a minor role. ISW1b and Chd1 make additive contributions to dinucleosome resolution. Set2-mediated H3-K36 trimethylation contributes to ISW1b-mediated dinucleosome separation.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Olesya I. I. Volokh, Anastasia L. L. Sivkina, Andrey V. V. Moiseenko, Anna V. V. Popinako, Maria G. G. Karlova, Maria E. E. Valieva, Elena Y. Y. Kotova, Mikhail P. P. Kirpichnikov, Timothy Formosa, Vasily M. M. Studitsky, Olga S. S. Sokolova
Summary: In this study, the effects of curaxin CBL0137 on nucleosome unfolding by FACT were analyzed. It was found that curaxin can induce FACT-dependent nucleosome unfolding and trap FACT in the chromatin of cancer cells. The obtained models suggest novel mechanisms of nucleosome unfolding by FACT and c-trapping by curaxins.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Sangram Kadam, Kiran Kumari, Vinoth Manivannan, Shuvadip Dutta, Mithun K. K. Mitra, Ranjith Padinhateeri
Summary: The authors provide a quantitative description of chromatin as bead-spring polymers, predicting the 3D size of chromatin beads and quantifying their stretchability, bendability, and softness. They systematically coarse-grain chromatin using Micro-C data and derive essential quantities for polymer representation. They also challenge the prevailing notion by showing that chromatin beads must be considered soft particles that can overlap, and in doing so, they derive an effective inter-bead soft potential and quantify an overlap parameter. Additionally, they analyze bond lengths and bond angles to gain insights into chromatin folding and local bendability.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Yuwei Cao, Hui Wang, Han Zhao, Xu Yang
Summary: This paper presents a model-free stereo calibration method for binocular fisheye cameras based on neural networks, which can effectively solve the problem of barrel distortion and preserve the advantages of the wide field of view of fisheye cameras.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Carlos E. Puerto Galvis, Cristian C. Granados, Vladimir V. Kouznetsov, Mario A. Macias
Summary: The Bischler-Napieralski reaction of N-phenylethyl cinnamamides was studied in acetonitrile and [bmim]PF6, showing significant effects on the isolated products depending on the starting materials and solvent. The use of [bmim]PF6 as a reaction medium led to the formation of hexafluorophosphate salts, while acetonitrile resulted in the isolation of free base products. X-ray crystallographic analysis revealed different conformers and structural stabilities in the two crystal structures.
NEW JOURNAL OF CHEMISTRY
(2021)
Article
Chemistry, Physical
Zhan-Yun Zhang, Ding Peng, Lihong Liu, Lin Shen, Wei -Hai Fang
Summary: We propose machine learning models that can predict experimental hydration free energies of molecules without requiring any specific atom, bond, or geometry features as input. Four different types of physically inspired descriptors are used for the predictions. The models, based on the FreeSolv database with around 600 samples, outperform most traditional approaches and other prediction methods using molecular fingerprints. These models are also capable of predicting hydration free energies for new compounds with elements or fragments not seen in the training set. The importance of the descriptors, the impact of dissociation energies of specific covalent bonds, and the presence of outliers with large prediction errors are discussed.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Julien Soudet, Nissrine Beyrouthy, Anna Marta Pastucha, Andrea Maffioletti, Dario Menendez, Zahra Bakir, Francoise Stutz
Summary: In this study, the researchers developed a genetic screen to identify new factors involved in Antisense-Mediated Transcription Interference (AMTI). They found that the HIR histone chaperone complex is involved in repressing the promoters of SAGA-dependent genes through antisense non-coding transcription. However, the presence of antisense transcription at gene promoters is not sufficient to determine the mode of gene regulation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Physical
Andres Cordoba
JOURNAL OF PHYSICAL CHEMISTRY B
(2018)
Correction
Chemistry, Physical
Andres Cordoba
JOURNAL OF PHYSICAL CHEMISTRY B
(2018)
Article
Chemistry, Physical
Joshua Lequieu, Andres Cordoba, Joshua Moller, Juan J. de Pablo
JOURNAL OF CHEMICAL PHYSICS
(2019)
Article
Chemistry, Physical
Andres Cordoba, Jay D. Schieber, Tsutomu Indei
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Mechanics
Diego Becerra, Andres Cordoba, Maria Katzarova, Marat Andreev, David C. Venerus, Jay D. Schieber
JOURNAL OF RHEOLOGY
(2020)
Article
Polymer Science
Diego Becerra, Andres Cordoba, Jay D. Schieber
Summary: The study using the discrete slip-link model (DSM) reveals nonuniversality in the nonlinear rheology of polymer melts at large strain rates during the inception of shear flow, despite the theory predicting universal behavior for maximum shear stress and strain at maximum stress based on entanglement activity and Kuhn steps. Primitive path stretching is shown to correspond to the transition of strain-rate-free values to values that scale with dimensionless strain rate. Additionally, differences in scaling exponents for melt and solution data suggest variations in steady-state shear stress, with DSM showing agreement with melt data.
Article
Mechanics
Jay D. Schieber, Andres Cordoba
Summary: This study uses straightforward energy and entropy balances to test the thermodynamic consistency of microstructural rheological models, identifying requirements for non-negative entropy production and adherence to the second law of thermodynamics. Several illustrative examples show that models using relaxation functions proportional to the free energy gradient are easier to check for compliance, while models using other types of relaxation functions may violate thermodynamic laws.
Article
Chemistry, Physical
Andres Rojano, Andres Cordoba, Jens H. Walther, Harvey A. Zambrano
Summary: A comprehensive understanding of fluid dynamics of dilute electrolyte solutions in nanoconfinement is essential to develop more efficient nanofluidic devices. In nanoconduits, the electrical double layer can occupy a considerable part of the channel cross-section, therefore the transport properties of a nanoconfined electrolyte solution can be altered by interfacial phenomena such as the charge inversion (CI).
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Mechanics
Andres Cordoba, Jay D. Schieber
Summary: A complete error propagation procedure for passive microrheology is demonstrated, incorporating statistical uncertainty in autocorrelations for any time series data and accounting for correlation in bead position data. Neglecting the correlation in the bead position data can lead to underestimation of the error in the mean-squared displacement of the probe bead by a factor of about 20.
Article
Chemistry, Multidisciplinary
Joan M. Montes de Oca, Johnson Dhanasekaran, Andres Cordoba, Seth B. Darling, Juan J. de Pablo
Summary: Janus nanopores show promise as ionic current rectifiers, with efficiency increasing as their diameter decreases, but little is known about the underlying transport processes under experimental conditions. Molecular simulations with explicit water and ions reveal previously unknown features, leading to a proposed model explaining ionic current rectification in Janus pores.
Article
Chemistry, Physical
Andres Cordoba, Joan M. Montes de Oca, Johnson Dhanasekaran, Seth B. Darling, Juan J. de Pablo
Summary: Bipolar nanochannels with charged nanoparticles can significantly enhance current rectification, potentially providing new opportunities for designing nanopore membrane-nanoparticle systems for energy storage.
MOLECULAR SYSTEMS DESIGN & ENGINEERING
(2023)
Article
Computer Science, Interdisciplinary Applications
Jeffrey G. Ethier, Andres Cordoba, Jay D. Schieber
Summary: Prior studies have demonstrated the accuracy of the discrete slip-link model (DSM) in predicting the rheology of entangled polymer systems. This work discusses the implementation of the fixed slip-link model and the clustered fixed slip-link model in Python, showing that Python can also utilize GPUs for fast quantitative rheological predictions. The developed pyDSM code allows for easy-to-use GPU computing and can be integrated with other simulation or data analysis software. Evaluation: 8/10
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Mechanics
Diego Becerra, Andres Cordoba, Jens H. Walther, Harvey A. Zambrano
Summary: Through atomic-level simulations, it is found that graphene coating significantly enhances water flow in nanochannels compared to hexagonal boron nitride (hBN) coating. The natural undulations of graphene coating further enhance water flow.
Article
Mechanics
Andres Cordoba, Jay D. Schieber
Summary: In this study, the dynamics and stability of a swarm of microswimmers are examined using a thermodynamically compliant microswimmer model. The research findings show that microswimmers in the swarm can swim much faster than when alone in an infinite sea, and the crystalline arrangement of the swarm plays a crucial role in the hydrodynamic interaction between swimmers. Moreover, the study reveals that hydrodynamic torques have a stabilizing effect on swarms of pullers but destabilize swarms of pushers. By considering fuel consumption and high order hydrodynamic interactions, the full dynamics of the swarm's stability are investigated.
Article
Biophysics
Andres Cordoba, Daniel M. Hinckley, Joshua Lequieu, Juan J. de Pablo
BIOPHYSICAL JOURNAL
(2017)