Article
Engineering, Multidisciplinary
Hongyang Cheng, Anthony R. Thornton, Stefan Luding, Andrew L. Hazel, Thomas Weinhart
Summary: The finite element method (FEM) is commonly used for modeling continuum media, while the discrete element method (DEM) is used for discrete systems. This paper introduces the coupling between discrete and continuum methods by mapping discrete particle data onto smooth fields. The authors found that using this coarse-graining approach leads to more accurate results, reduced energy generation, and less numerical dissipation.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2023)
Article
Materials Science, Multidisciplinary
A. A. Madadi, A. R. Khoei
Summary: In this paper, a multi-scale method is proposed to couple atomistic and coarse-grained systems for modeling the mechanical properties of materials with defects and heterogeneity. By combining Molecular Dynamics analysis with a coarse-grained approach, the method reduces computational costs and allows for the effective study of material behavior and properties.
COMPUTATIONAL MATERIALS SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Giuliana Giunta, Gerardo Campos-Villalobos, Marjolein Dijkstra
Summary: Colloidal nanoparticles can self-assemble into superstructures with distinctive properties. This study proposes a machine-learning approach to construct effective coarse-grained many-body interaction potentials for investigating the self-assembly behavior of complex colloidal systems. The key advantage of this method is its generality.
Article
Physics, Multidisciplinary
Rick Bebon, Ulrich S. Schwarz
Summary: The article explores the computation of complex energy landscapes in biological systems, particularly their effects on first-passage times (FPTs). The authors propose a method to identify the most relevant features of energy landscapes by coarse-graining the Fokker-Planck equation to a master equation and decomposing its FPTs iteratively. They apply this method to the electrostatic interaction between two nonmuscle myosin II (NM2) rods and identify the most relevant energy barriers for their self-assembly into NM2 minifilaments and how they change under force.
NEW JOURNAL OF PHYSICS
(2022)
Article
Chemistry, Physical
Nathan Hostettler, Pascal Hubert
Summary: The addition of graphene particles significantly improves the electrical properties of thermoset resin, making it suitable for damage and strain tracking. However, the increase in electrical properties depends on the amount and purity of graphene particles, which are usually expensive. To reduce the quantity needed for conduction, a self-assembly network of graphene particles was created using unsaturated polyester and polycaprolactone blends, resulting in a significant enhancement of DC and AC electrical conductivities. The optimized composition required only 1.4 wt% of graphene compared to the initial 8.2 wt%. These materials also showed excellent strain sensing capabilities at low applied voltage, making them reliable and cost-effective for self-sensing and damage tracking applications.
Article
Chemistry, Multidisciplinary
Jianhua Wang, Yuhui Wei, Ping Zhang, Yue Wang, Qinglin Xia, Xiaoguo Liu, Shihua Luo, Jiye Shi, Jun Hu, Chunhai Fan, Bin Li, Lihua Wang, Xingfei Zhou, Jiang Li
Summary: In this study, the folding processes of several multidomain DNA origami structures were visualized using atomic force microscopy under ambient annealing conditions in solution, revealing the coexistence of diverse transitional structures that might result in the same prescribed products. Based on experimental observations and energy landscape simulations, the heterogeneity of the folding pathways of multidomain DNA origami structures was proposed.
Article
Biochemical Research Methods
Giovanni B. Brandani, Cheng Tan, Shoji Takada
Summary: Nucleosomes, consisting of DNA wrapped around histone proteins, are fundamental units of Eukaryotic chromosomes that compact the genome and regulate gene expression. Molecular dynamics simulations have provided insights into the kinetics, structure, and influencing factors of nucleosome assembly. The study found that histones and DNA can form various non-canonical nucleosome conformations during the complex assembly process, which remains unclear in detail.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Engineering, Chemical
V. Brandt, J. Grabowski, N. Jurtz, M. Kraume, H. Kruggel-Emden
Summary: DEM-CFD is computationally demanding and limited to lab-scale systems, so coarse-graining approaches are used to summarize particles. This study compares force scaling models in different beds to eliminate influences and identifies optimal scaling rules based on physical parameters. It also analyzes fluidized beds to determine the suitability of scaling models for systems governed by both contact and hydrodynamic forces, providing recommendations for future simulations of industrial-scale particle systems.
Article
Chemistry, Multidisciplinary
Sanaz Panahandeh, Siyu Li, Bogdan Dragnea, Roya Zandi
Summary: This paper reveals the mechanism of viral shell growth by conducting a series of simulations, and explores how cargo-coat protein interactions can impact the structure and stability of the viral shells. The study finds that coat proteins can assemble around a nucleic acid core to form nonicosahedral structures, which are strained and can easily split into fragments. However, if the larger wild-type genome is available, these metastable nonicosahedral intermediates can be reassembled into stable icosahedral shells.
Article
Multidisciplinary Sciences
Oliver G. Hayes, Benjamin E. Partridge, Chad A. Mirkin
Summary: This study demonstrates the deliberate control of hierarchical assembly of protein-DNA materials by exploiting the chemical anisotropy of proteins and the programmability of DNA ligands. The introduction of orthogonal DNA interactions with disparate strengths onto specific geometric regions of a model protein leads to directional assembly and increased multi valency through DNA sequence design. The judicious DNA design not only directs assembly along a specific pathway but also influences distinct structural outcomes from a single pathway.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Shuang Wang, Xiaolin Xie, Zhi Chen, Ningning Ma, Xue Zhang, Kai Li, Chao Teng, Yonggang Ke, Ye Tian
Summary: The DNA-grafted nanoparticle serves as a programmable atom equivalent for assembling three-dimensional superlattice with novel properties, allowing for the exploration of assembly strategies and mechanisms, as well as future applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Engineering, Electrical & Electronic
Zefang Han, Shangguan Hong, Zhang Xiong, Xueying Cui, Wang Yue
Summary: With the development of CT technology, reducing radiation dose in CT scans is a concern due to potential damage. A new approach, called CMFHGAN, is proposed to improve the quality of low-dose CT scans by effectively fusing features of different scales. The experiments show that CMFHGAN outperforms existing denoising algorithms.
SIGNAL PROCESSING-IMAGE COMMUNICATION
(2023)
Article
Nanoscience & Nanotechnology
Shuo Yang, Wenyan Liu, Yuwei Zhang, Risheng Wang
Summary: In this study, a new strategy utilizing DNA origami tiles and cation-controlled surface diffusion was employed to assemble gold nanorods into 1D and 2D arrays, with a novel pattern transfer method introduced for further manipulation. The results demonstrate the potential application of this approach in constructing complex superstructures with high yield and minor structural damage.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Chemistry, Multidisciplinary
Yuxiang Dong, Jiliang Liu, Xuanzhao Lu, Jialin Duan, Liqi Zhou, Lizhi Dai, Min Ji, Ningning Ma, Yong Wang, Peng Wang, Jun-Jie Zhu, Qianhao Min, Oleg Gang, Ye Tian
Summary: Self-assembly processes are important for fabricating complexly organized nanomaterials, but often limited in creating structures with multiscale order. In this study, a two-stage assembly strategy is introduced to successfully form complexly organized nanoparticle crystals.
Article
Engineering, Chemical
M. J. A. de Munck, J. B. van Gelder, E. A. J. F. Peters, J. A. M. Kuipers
Summary: Computational Fluid Dynamics-Discrete Element Method (CFD-DEM) is a numerical tool used for detailed fluidized bed studies. To overcome its computational expense, coarse-graining techniques have been developed. In this study, we compared the effectiveness of different coarse-graining scaling laws in characterizing the original system. We also demonstrated the usefulness of a continuous two-way smoothing function in achieving grid-independent solutions in CFD-DEM simulations.
CHEMICAL ENGINEERING SCIENCE
(2023)
Article
Chemistry, Physical
Jordan Juritz, Jenny M. Poulton, Thomas E. Ouldridge
Summary: The production of sequence-specific copolymers using copolymer templates is crucial for the synthesis of complex biological molecules and synthetic chemical complexes. Overcoming product inhibition has been a major challenge in implementing templated copying of copolymers. In this study, we develop coarse-grained models and use stochastic simulation to analyze copolymerization on a finite-length template. We demonstrate that product inhibition hinders reliable template copying and propose a solution to achieve cyclic production of polymer copies by disrupting copy-template bonds and weakening the final copy-template bond. This research opens up possibilities for engineering synthetic copying systems that operate autonomously.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemical Research Methods
Alicia Climent-Catala, Thomas E. Ouldridge, Guy-Bart Stan, Wooli Bae
Summary: Synthetic RNA systems have advantages over protein-based networks in terms of faster response, increased specificity, and programmability. In this study, we developed an in vitro RNA toggle switch using RNA aptamers to inhibit the transcriptional activity of two different RNA polymerases. The switch was successfully controlled by adding DNA sequences. The results demonstrated that the RNA-based toggle switch has potential applications in synthetic biology.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Joshua M. Lawrence, Yutong Yin, Paolo Bombelli, Alberto Scarampi, Marko Storch, Laura T. Wey, Alicia Climent-Catala, Geoff S. Baldwin, Danny O'Hare, Christopher J. Howe, Jenny Z. Zhang, Thomas E. Ouldridge, Rodrigo Ledesma-Amaro
Summary: This study developed a strong redox-responsive promoter and derived a mutant promoter library with varying strengths. Using these tools, researchers demonstrated the electrochemical activation of gene expression in electrogenetic systems, providing new means for the design and improvement of electrogenetics.
Article
Biochemistry & Molecular Biology
Sophie Hertel, Richard E. Spinney, Stephanie Y. Xu, Thomas E. Ouldridge, Richard G. Morris, Lawrence K. Lee
Summary: The physical mechanisms underlying DNA hybridization rates are still not well understood. Secondary structure is one factor that affects the rates, but there are other factors at play. Research has shown that a higher number of Watson-Crick pair repetitions increases the number of initial states capable of proceeding to full hybridization, with the stability of these pairings dictating the likelihood of progression.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Biology
Susanna Manrubia, Jose A. Cuesta, Jacobo Aguirre, Sebastian E. Ahnert, Lee Altenberg, Alejandro V. Cano, Pablo Catalan, Ramon Diaz-Uriarte, Santiago F. Elena, Juan Antonio Garcia-Martin, Paulien Hogeweg, Bhavin S. Khatri, Joachim Krug, Ard A. Louis, Nora S. Martin, Joshua L. Payne, Matthew J. Tarnowski, Marcel Weiss
PHYSICS OF LIFE REVIEWS
(2022)
Article
Chemistry, Multidisciplinary
Joakim Bohlin, Andrew J. Turberfield, Ard A. Louis, Petr Sulc
Summary: We explored the design space for self-assembled multicomponent objects, ranging from unique building blocks to minimum number of distinct building blocks defining the target structure. By using patchy particle simulations, we analyzed the assembly dynamics of different solutions and their influence on the kinetics and yield of the target assembly. Our findings show that resource-saving solutions with minimum distinct blocks can perform just as well or faster than designs with unique building blocks. We also designed multifarious structures by sharing building blocks between different targets, and investigated the realization of multicomponent shapes using DNA nanostructures as building blocks through coarse-grained DNA simulations.
Article
Chemistry, Physical
Benjamin Qureshi, Jordan Juritz, Jenny M. Poulton, Adrian Beersing-Vasquez, Thomas E. Ouldridge
Summary: Copolymers play a vital role in both living and synthetic systems. We have developed a general method for analyzing copolymerization processes, which can be used to derive thermodynamic, kinetic, and statistical quantities from the model definition.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Laura Dal Compare, Flavio Romano, Jared A. Wood, Asaph Widmer-Cooper, Achille Giacometti
Summary: The phase diagram of hard helices is different from that of hard rods due to the presence of chiral screw phases. The addition of short-range attractive interactions to a fraction of the sites forming the hard helices results in different temperature regimes. The location of the transition lines does not have a simple dependence on the fraction of attractive beads.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Tomislav Plesa, Alexander Dack, Thomas E. Ouldridge
Summary: A central goal of synthetic biology is to design molecular controllers that can manipulate intracellular networks. Integral-feedback controllers (IFCs) have been proposed to control molecular abundances in the absence of detailed knowledge about intracellular networks. These controllers can maintain accuracy despite the uncertainties in the networks, but stability is also crucial.
JOURNAL OF MATHEMATICAL CHEMISTRY
(2023)
Article
Physics, Fluids & Plasmas
Ian Seet, Thomas E. Ouldridge, Jonathan P. K. Doye
Summary: Landauer's principle sets a lower limit on the work required for logically irreversible operations, which can be overcome by using logically reversible gates. This paper presents the design and simulation of molecular mechanical logic gates that approach the limits of thermodynamic reversibility, even in the presence of thermal noise. The study demonstrates the feasibility of constructing and simulating arbitrary combinatorial reversible circuits with these gates.
Article
Multidisciplinary Sciences
Vaibhav Mohanty, Sam F. Greenbury, Tasmin Sarkany, Shyam Narayanan, Kamaludin Dingle, Sebastian E. Ahnert, Ard A. Louis
Summary: Phenotype robustness is crucial for the neutral exploration of novel phenotypic variation. The maximal phenotype robustness occurs when genotypes are organized as bricklayer's graphs. The RNA secondary structure and the hydrophobic-polar (HP) model for protein folding can exhibit the maximum phenotype robustness.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Physics, Fluids & Plasmas
Vaibhav Mohanty, Ard A. Louis
Summary: Investigated the robustness of spin glasses in the glassy phase, finding high robustness and topological properties that scale similarly to other systems.
Article
Biochemical Research Methods
Alicia Climent-Catala, Ivan Casas-Rodrigo, Suhasini Iyer, Rodrigo Ledesma-Amaro, Thomas E. Ouldridge
Summary: This study investigates the performance of RNA light-up aptamers as transcriptional fluorescent reporters and compares them to protein-based reporters. The researchers found that RNA light-up aptamers exhibit suitable characteristics as transcriptional reporters over time and at the single-cell level, with higher variability in a population compared to protein-based reporters. Additionally, these RNA aptamers may offer faster dynamics compared to fluorescent proteins in E. coli. The implementation of these transcriptional reporters can facilitate transcription-based studies and expand the use of RNA-based circuits in bacterial cells.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Physics, Multidisciplinary
Thomas E. Ouldridge, David H. Wolpert
Summary: This paper investigates the operational constraints of real-world computers that result in nonzero entropy production. The author first derives the nonzero entropy production caused by the locality and periodicity constraints in deterministic finite automata (DFA). The author then classifies the languages recognized by DFA into two categories based on the presence or absence of nonzero entropy production. The paper also demonstrates the thermodynamic advantages of implementing a DFA with a physical process that is agnostic about the inputs it processes.
NEW JOURNAL OF PHYSICS
(2023)
