Article
Chemistry, Physical
Yaroslav Groda, Maxym Dudka, Alexei A. Kornyshev, Gleb Oshanin, Svyatoslav Kondrat
Summary: Mapping the charging theory of supercapacitors with nanostructured electrodes onto lattice models of statistical physics can reveal generic features of capacitive energy storage in such systems and provide analytical solutions for developing new physical insights. The study found a remarkable agreement between analytical theory and simulations, and discovered a correlation between ion ordering inside a pore and the ability to store energy.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Review
Biochemical Research Methods
Andrea Raffo, Jonas Paulsen
Summary: The three-dimensional organization of chromatin is essential for gene regulation and cellular processes. Hi-C and related techniques offer a detailed understanding of spatial proximities in the nucleus, but data analysis is complicated due to a lack of mathematical frameworks. Recognizing and analyzing geometric patterns in Hi-C data has emerged as a powerful approach. This review summarizes algorithms for automatic recognition and analysis of geometric patterns in Hi-C data and their relationship with chromatin structure, classifying them based on data representation and pattern recognition paradigms. Finally, challenges and future directions are outlined.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Polymer Science
Chia-Cheng Chu, Pai-Yi Hsiao
Summary: This article proposes a two-stage model to explain the phenomena of chain expansion released from a confining cavity. In the first stage, the chain is assumed to expand as a sphere, while in the second stage it expands like a coil. The kinetic equations for the variation of chain size are derived in the two stages by balancing the rate of the free energy change with the rate of energy dissipation. Langevin dynamics simulations are performed to examine the theory. The simulation results support the theory and reveal that the expansion process is dominated by the second stage, confirming the predicted curve for coil expansion.
Article
Biochemical Research Methods
Ke Zhang, Chenxi Wang, Liping Sun, Jie Zheng
Summary: HiCoEx is an end-to-end framework for explainable prediction of gene co-expression from Hi-C data, utilizing a graph neural network. It applies a graph attention mechanism to a gene contact network inferred from Hi-C data in order to learn gene representations for supervised prediction of co-expression in a task-specific manner. The model is able to automatically learn gene representations from 3D genomics signals and capture meaningful biological patterns to improve prediction accuracy.
Article
Biochemistry & Molecular Biology
Moritz Bauer, Bernhard Payer, Guillaume J. Filion
Summary: The spatial organization of genomes is closely related to transcription, and understanding whether gene activity is a cause or consequence of genome folding is an important research objective. Recent studies on the structural changes associated with X-chromosome inactivation and reactivation shed light on this cause-consequence relationship between genome conformation and transcription.
Article
Multidisciplinary Sciences
Andriy Goychuk, Deepti Kannan, Arup K. Chakraborty, Mehran Kardar
Summary: From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate. Moreover, chromatin motion varies with genomic coordinate, pointing toward a heterogeneous pattern of active processes along the sequence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Marine & Freshwater Biology
Didi Jin, Chao Li, Xiao Chen, Adam Byerly, Naomi A. Stover, Tengteng Zhang, Chen Shao, Yurui Wang
Summary: This study assembled the MAC genome of Euplotes aediculatus, a representative species in Spirotrichea, and found high fragmentation and the presence of nanochromosomes. The expansion of gene families associated with chitin metabolism and FoxO signaling pathway suggests their potential roles in adaptation and survival strategies. Furthermore, the occurrence of programmed ribosomal frameshift genes with a conservative motif suggests their importance in cellular regulation processes.
MARINE LIFE SCIENCE & TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Lindsay Lee, Hongyu Yu, Bojing Blair Jia, Adam Jussila, Chenxu Zhu, Jiawen Chen, Liangqi Xie, Antonina Hafner, Shreya Mishra, Duan Dennis Wang, Caterina Strambio-De-Castillia, Alistair Boettiger, Bing Ren, Yun Li, Ming Hu
Summary: Researchers have developed a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH) which can accurately identify chromatin loops. SnapFISH is capable of processing multiplexed DNA FISH data and identifying known chromatin loops. It also produces consistent results across diverse imaging technologies.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Jehoshaphat Oppong Mensah, Aaron Boakye, Michael Laryea, Edward Ntim Gasu, Lawrence Sheringham Borquaye
Summary: This study used molecular dynamics simulation to investigate the membrane selectivity of antimicrobial peptide Maximin 1. The results showed that Maximin 1 interacts more strongly with the bacterial membrane due to electrostatic attraction and certain residues and structural characteristics play a crucial role in the adsorption and penetration of the bacterial membrane.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Plant Sciences
Senjie Lin, Bo Song, David Morse
Summary: The genome architecture, evolution, and function in dinoflagellates are enigmatic and continuously inspire scientific quests. Recent research has shed light on the spatial organization of symbiodiniacean genomes, hinting at potential evolutionary trends in chromosome number decrease and length increase. Despite remaining mysteries, these findings provide new starting points for future inquiries.
JOURNAL OF PHYCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Zekun Huang, Wanlong Huang, Xiaolin Liu, Zhaofang Han, Guangjian Liu, Grace Afumwaa Boamah, Yi Wang, Feng Yu, Yang Gan, Qizhen Xiao, Xuan Luo, Nan Chen, Meng Liu, Weiwei You, Caihuan Ke
Summary: The nautilus, known as a living fossil, is endangered and may face extinction. The lack of genomic information hinders understanding of its biology and evolution, but research reveals strong adaptability and long-term survival in its evolutionary process.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Biology
Hiroyuki Shimoji, Shigeto Dobata
Summary: Reproductive division of labour is a characteristic of eusocial insects, but can be disrupted by reproductive potential of otherwise sterile nest-mates. Dominance hierarchy plays a crucial role in regulating reproduction in some species, and dominance hierarchies in eusocial insects involve more individuals than in vertebrates, requiring unique selective forces. This article provides an overview of studies on dominance hierarchies in eusocial insects, specifically focusing on paper wasps and ponerine ants. It explains the emergence of dominance hierarchies as a self-organizing process through individual memory and local behavioral interactions, which can be captured using network analyses. The adaptive significance of dominance hierarchies is also discussed from the perspective of sterile subordinates, emphasizing the importance of kin selection.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Materials Science, Multidisciplinary
Yingbin Chen, Luying Huang, Traian Dumitrica, Hao Xu
Summary: In this study, we used molecular simulations to investigate the anisotropic nonlinear bending of graphene with tilt GBs. We found that the anisotropy and nonlinearity are caused by the out-of-plane protrusions of the dislocation cores at the GBs. We also explored the elastic responses of curved graphene structures controlled by GBs and established the coupling between the elastic modulus and local curvature near the GBs. Our findings provide useful references for designing 3D graphene structures using GBs and can be applied to other 2D materials.
DIAMOND AND RELATED MATERIALS
(2022)
Article
Biochemical Research Methods
Ranylson Marcello L. Savedra, Marlene Notelio B. L. de Morais, Melissa F. Siqueira
Summary: This paper investigates the influence of solvents on the microstructure of polymer films. The comparison of two simulation methods reveals that solvents can reduce the length of oligomer chains and induce a more ordered chain distribution, affecting the microstructure of the films.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Biochemical Research Methods
Zhenjia Wang, Yifan Zhang, Chongzhi Zang
Summary: BART3D is a computational method for inferring TRs associated with genome-wide differential chromatin interactions by comparing Hi-C maps from two states, demonstrating its ability to detect relevant TRs from dynamic Hi-C profiles with TR perturbation or cell differentiation, making it a useful tool in 3D genome data analysis and functional genomics research.
Article
Chemistry, Multidisciplinary
Dongfang Wang, Lei Yu, Chao-Min Huang, Gaurav Arya, Shuai Chang, Yonggang Ke
Summary: This article introduces a modular design method to programmatically adjust the shapes of DNA origami nanomachines. By changing the length of DNA units and using different combinations of trigger DNA strands, controlled transformations of the overall dimensions and curvatures of DNA origami can be achieved. This modular design has potential applications in more sophisticated molecular nanorobots and smart drug delivery nanocarriers.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Brian Hyun-jong Lee, Gaurav Arya
Summary: In this study, the mechanism of assembly of nanocubes grafted with short-chain molecules was computationally investigated. It was found that the assembly pathway of nanocubes is very rugged involving multiple energy barriers and metastable states. The assembly mechanism is dominated by sliding motion of nanocubes relative to each other punctuated by their local dissociation at grafting points involving lineal separation and rolling motions.
Article
Chemistry, Multidisciplinary
Yilong Zhou, Tsung-Yeh Tang, Brian Hyun-jong Lee, Gaurav Arya
Summary: Trapping surface-functionalized faceted nanoparticles at fluid-fluid interfaces can control particle orientation and facilitate their assembly into unique one- and two-dimensional superstructures. By tuning the graft density and differences in miscibility, nanocubes can be induced into different orientations. These orientationally constrained nanocubes can assemble into various unusual structures, which have potential applications in plasmonics, optics, catalysis, and membranes.
Article
Cell Biology
Vanessa Simoes, Blanche K. Cizubu, Lana Harley, Ye Zhou, Joshua Pajak, Nathan A. Snyder, Jonathan Bouvette, Mario J. Borgnia, Gaurav Arya, Alberto Bartesaghi, Gustavo M. Silva
Summary: Protein ubiquitination is an important process that regulates protein synthesis, function, and fate. The E2 Rad6 associates and modifies ribosomes during stress, and its activity is redox regulated. This study provides insights into the role and regulation of E2 enzymes in the ubiquitination pathway and reveals the physiological role of Rad6 in translation, antioxidant defense, and stress adaptation.
Article
Biochemistry & Molecular Biology
Joshua Pajak, Gaurav Arya
Summary: The bacterial FtsK motor utilizes ATP to translocate double-stranded DNA during cell division. Through long timescale simulations and free-energy calculations, the molecular mechanisms underlying coordinated DNA translocation in FtsK are revealed. Each ATP-bound subunit of the motor conforms to the helical pitch of DNA, and ATP hydrolysis causes a subunit to lose grip of DNA, resulting in unidirectional DNA translocation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Kyle Barcus, Po-An Lin, Yilong Zhou, Gaurav Arya, Seth M. Cohen
Summary: Polymer-grafted metal-organic frameworks (MOFs) combine the properties of MOFs and polymers into a matrix-free composite material. The choice of polymer affects the physical properties of the monolayers, and poly(methyl acrylate) is more suitable for producing robust, flexible monolayers. Molecular dynamics simulations provide insights into the orientation and ordering of MOFs in the monolayers, and the relationship between molecular weight and graft density of the polymer brush can be used for further optimization of mechanical strength, MOF weight fraction, and processability.
Article
Multidisciplinary Sciences
Yilong Zhou, Gaurav Arya
Summary: This research paper presents a method for self-assembling binary nanoparticle superlattices using fluid-fluid interfaces. By varying the size ratio, interaction strength, and miscibility of the nanoparticles with the fluids, different structures of 2D superlattices can be formed. The results suggest that the interfacial assembly approach is a versatile platform for fabricating 2D colloidal superlattices with tunable structure and properties.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Chunyang Zhou, Donglei Yang, Sebastian Sensale, Pranav Sharma, Dongfang Wang, Lei Yu, Gaurav Arya, Yonggang Ke, Pengfei Wang
Summary: This study reports a design method for controllable DNA molecular structures through controlled base stacking. Precise control over molecular conformation and transformation is achieved by programming stacking bonds within the junction. Dynamic transformations between different conformations are achieved through specific environmental and molecular stimulations.
Article
Chemistry, Multidisciplinary
Yuchen Wang, Sebastian Sensale, Miguel Pedrozo, Chao-Min Huang, Michael G. Poirier, Gaurav Arya, Carlos E. Castro
Summary: Biomolecular nanotechnology is used to mimic robotic capabilities in nanoscale systems, and DNA origami is an attractive method for creating complex nanorobotic devices. This study introduces a communication mechanism inspired by protein allostery to transmit signals between two distal dynamic components through steric interactions. The research demonstrates that one arm can regulate the motion range and conformational state of the distal arm, and signal transmission can be modulated by tuning thermal fluctuations and controlling the conformational states of the components.
Review
Nanoscience & Nanotechnology
Marcello DeLuca, Sebastian Sensale, Po-An Lin, Gaurav Arya
Summary: DNA nanotechnology is a rapidly developing field that utilizes DNA as a building material for nanoscale structures. This review discusses the prediction and control aspects of DNA nanotechnology, including molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. The current applications of artificial intelligence and machine learning in DNA nanotechnology are also addressed. The combination of experiments and modeling allows for control over device behavior and the design of molecular structures and dynamic devices. Weak areas in prediction ability are identified, and possible solutions are suggested.
ACS APPLIED BIO MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Yunqi Yang, Qinyi Lu, Yu Chen, Marcello DeLuca, Gaurav Arya, Yonggang Ke, Stefan Zauscher
Summary: DNA nanotechnology allows for the creation of precise and tunable nanostructures for biomedical applications. However, the stability of these structures is compromised in biological environments due to degradation by nucleases. This study demonstrates a strategy to enhance the stability of the structures by utilizing enzymatic polymerization to grow polynucleotide brushes on DNA nanostructures. The ability to control the spatial and temporal growth of these brushes offers potential applications in drug delivery and supramolecular assembly.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Wolfgang G. Pfeifer, Chao-Min Huang, Michael G. Poirier, Gaurav Arya, Carlos E. Castro
Summary: Recent advances in structural DNA nanotechnology have led to the development of design tools that push the limits of complexity and simplify the design process. MagicDNA 2.0, an updated design tool, automates the design of free-form 3D geometries using coarse-grained molecular dynamics simulations. This approach allows for versatile control and automation, leading to the successful fabrication of complex DNA origami structures.
Article
Chemistry, Multidisciplinary
Marcello DeLuca, Wolfgang G. G. Pfeifer, Benjamin Randoing, Chao-Min Huang, Michael G. G. Poirier, Carlos E. E. Castro, Gaurav Arya
Summary: Control over the patterning of materials at the mesoscale to microscale level is of interest to the soft matter community. Inspired by DNA origami rotors, a 2D lattice of spinning rotors with discrete orientational states and interactions with neighbors is introduced. Monte Carlo simulations reveal that these rotor lattices exhibit various ordering behaviors and morphologies influenced by design parameters. Real DNA origami rotors are fabricated, demonstrating ordered and disordered phases, and showing the potential for responsive organization in structurally nanomaterials.
Article
Chemistry, Physical
Yilong Zhou, Sigbjorn Loland Bore, Andrea R. Tao, Francesco Paesani, Gaurav Arya
Summary: This article introduces a machine-learning approach to develop a many-body potential for describing effective interactions between spherical polymer-grafted nanoparticles in a polymer matrix. The potential significantly reduces computational cost and enables simulation of various assembly behaviors.
NPJ COMPUTATIONAL MATERIALS
(2023)
Article
Physics, Fluids & Plasmas
Sebastian Sensale, Pranav Sharma, Gaurav Arya
Summary: In this paper, we study the diffusion-mediated binding of molecules under the influence of confining potentials and derive analytical expressions for the mean binding time. We demonstrate the utility of this theory in improving the communication speed of DNA walkers and provide a way to optimize the rate of signal propagation for nanoscale sensing and computing applications. This research has broad applicability and significance in understanding molecular interactions and communication processes.
