Article
Chemistry, Multidisciplinary
Raghu Pradeep Narayanan, Jonah Procyk, Purbasha Nandi, Abhay Prasad, Yang Xu, Erik Poppleton, Dewight Williams, Fei Zhang, Hao Yan, Po-Lin Chiu, Nicholas Stephanopoulos, Petr Sulc
Summary: This study presents a combination of experimental and computational modeling tools for the design and characterization of protein-DNA hybrid nanostructures. The tools can optimize the design and validate experimental results, facilitating the design of complex nanostructures.
Review
Physics, Multidisciplinary
Tanja Schilling
Summary: This article discusses the construction of coarse-grained models for systems out of thermal equilibrium, including both equilibrium and non-equilibrium coarse-graining methods and numerical schemes.
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
(2022)
Review
Chemistry, Multidisciplinary
Li-Dan Zhao, Xia Yang, Xia Zhong, Ying Zhuo
Summary: DNA walkers, composed of driving power, walking strands and tracks, are programmable molecular machines with diverse structures. They can generate and amplify signals under specific external stimuli, such as strand displacement strategies, enzymatic reactions, and environmental condition stimulus. DNA walker-based ECL biosensors combine ECL technology and bio-identification strategies to achieve ultrasensitive detection for diverse targets through multiple identification and recycling methods.
Article
Chemistry, Multidisciplinary
Emma. H. H. Wolpert, Kim. E. E. Jelfs
Summary: The packing behavior of molecules has significant implications for their applications as functional molecular materials. However, predicting the crystal structure of organic molecules is a challenging problem in crystal engineering. This study focuses on the packing behavior of porous organic cages (POCs) and proposes a novel method to predict their solid-state phase behavior using a simplified model. The results demonstrate the influence of chemical functionality on the solid-state phase formation of POCs and pave the way for the development of design rules.
Article
Chemistry, Physical
Yancheng Du, Jing Pan, Hengming Qiu, Chengde Mao, Jong Hyun Choi
Summary: The research analyzes the motion dynamics of DNA dynamic walkers by adopting a random walk model, identifying four different migration modes and elucidating their characteristics in relation to mean-squared displacement. Experimental results validate theoretical predictions and explore the impact of various factors on the behaviors of DNA walkers.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Thermodynamics
Shuai Wang, Yansong Shen
Summary: A coarse-grained CFD-DEM model is developed to simulate dense gas-solid reacting flow, which significantly reduces computational costs. This research is important for simulating dense gas-solid reacting flow in chemical reactors.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2022)
Article
Physics, Multidisciplinary
Irenee Frerot, Antonio Acin
Summary: This work demonstrates the application of self-testing in many-body systems and proves that membership in a set of (entangled) quantum states can be determined based on self-testing in the Bell scenario.
PHYSICAL REVIEW LETTERS
(2021)
Article
Engineering, Geological
Jidong Teng, Jianlong Liu, Sheng Zhang, Daichao Sheng
Summary: This study investigates frost heave in coarse-grained soils caused by vapour transfer through laboratory experiments and numerical simulations. The results demonstrate significant frost heave in coarse-grained soil specimens, and the frost heave ratio increases with time. A numerical model is developed to simulate ice formation and frost heave, which shows good agreement with the experimental results. This study provides a novel explanation for the frost heave mechanism in coarse-grained soils.
Article
Chemistry, Multidisciplinary
Ilias Patmanidis, Paulo C. T. Souza, Selim Sami, Remco W. A. Havenith, Alex H. de Vries, Siewert J. Marrink
Summary: Self-assembly is a widely observed process, but understanding its dynamic pathways and molecular details of the final structures is challenging. This study addresses this problem by using coarse-grained modeling and successfully optimizing parameters for a cyanine dye. Simulations provide information on the time-dependent local arrangement of the dye during self-assembly, and guidelines for designing and optimizing similar self-assembling nanomaterials.
NANOSCALE ADVANCES
(2022)
Article
Chemistry, Physical
Jonah Procyk, Erik Poppleton, Petr Sulc
Summary: The emerging field of hybrid DNA-protein nanotechnology shows promise for novel materials, but faces challenges in design and computational study. A coarse-grained DNA/RNA-protein model is introduced to aid in design and analysis, with the goal of facilitating hybrid nanomaterial design and enabling study of biological complexes.
Review
Biochemistry & Molecular Biology
Tiedong Sun, Vishal Minhas, Nikolay Korolev, Alexander Mirzoev, Alexander P. Lyubartsev, Lars Nordenskiold
Summary: This review presents some well-developed bottom-up coarse-graining methods for effective modeling of DNA properties, such as DNA flexibility, conformation, melting, and condensation, based on underlying atomistic force field simulations. These methods separate fast and slow dynamic processes in molecular systems and construct coarse-grained Hamiltonian using pair-wise additive potential for efficiency in computer simulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Medicinal
Subhamoy Mahajan, Tian Tang
Summary: This article presents a fully automated algorithm that can coarse-grain the molecular structure of polyethylenimine (PEI) from its all-atom simulation, allowing for replication of experimental data and computational inference of chemical structures. The developed methodology can be extended to other polymers.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Polymer Science
Riccardo Alessandri, Juan J. de Pablo
Summary: The properties of soft electronic materials depend on the coupling of electronic and conformational degrees of freedom. Traditional approaches for describing these properties require multiscale methods, which can access electronic properties and sample the conformational space of soft materials. In this study, a machine learning method combined with coarse-grained techniques is proposed to replace the traditional backmapping-based approaches without sacrificing accuracy.
Article
Chemistry, Physical
Jaehyeok Jin, Kenneth S. Schweizer, Gregory A. Voth
Summary: The first paper of this series demonstrated the scalability of excess entropy for both fine-grained and coarse-grained systems. However, a more precise determination of the scaling relationship was not possible due to its semi-empirical nature. In this second paper, an analytical scaling relation for excess entropy is derived for bottom-up coarse-grained systems. By constructing effective hard sphere systems at the single-site resolution, the dynamics and excess entropy of the target coarse-grained systems can be accurately approximated.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Chemistry, Multidisciplinary
Zhenghao Zhu, Xubo Luo, Stephen J. Paddison
Summary: Ion-containing polymers have been extensively studied due to their potential as electrolytes in energy storage devices. Coarse-grained modeling is an efficient approach to explore the structural and dynamical properties of these materials. This review summarizes the current understanding and development of ion-containing polymers and provides insights into their design for improved performance in power source technologies.
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, Medicinal
Zhengyue Zhang, Jiri Sponer, Giovanni Bussi, Vojtech Mlynsky, Petr Sulc, Chad R. Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Summary: HJ is a crucial DNA structure involved in DNA repair, recombination, and DNA nanotechnology. Molecular dynamics simulations revealed complex conformational transitions of HJs, including previously unconsidered half-closed intermediates. This study provides detailed insights into the rearrangement process of HJs and opens up possibilities for more accurate computational studies of biological processes and nanomaterials involving HJs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Camilla Beneduce, Diogo E. P. Pinto, Petr Sulc, Francesco Sciortino, John Russo
Summary: This study investigates the nucleation process of a binary mixture of patchy particles designed to nucleate into a diamond lattice. By combining Gibbs-ensemble simulations and direct nucleation simulations, the role of the liquid-gas metastable phase diagram on the nucleation process is revealed. The strongest enhancement of crystallization is found to occur at an azeotropic point with the same stoichiometric composition of the crystal.
JOURNAL OF CHEMICAL PHYSICS
(2023)
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, Multidisciplinary
Yue Tang, Hao Liu, Qi Wang, Xiaodong Qi, Lu Yu, Petr Sulc, Fei Zhang, Hao Yan, Shuoxing Jiang
Summary: Moleculartessellation research aims to understand intricate patterns in nature and leverage them to create precise structures. This study presents a general method for constructing DNA origami tiles that form precise tessellation patterns. The study demonstrates the applicability of the method with various tile designs and tessellation patterns, opening up new opportunities for applications in metamaterial engineering, nanoelectronics, and nanolithography.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Diogo E. P. Pinto, Petr Sulc, Francesco Sciortino, John Russo
Summary: The control over self-assembly of complex structures, particularly at the colloidal scale, has been a significant challenge in material science. The formation of amorphous aggregates often disrupts the desired assembly pathway. In this study, we investigate the self-assembly problem of three Archimedean shells using patchy particles as model building blocks. By recasting the assembly problem as a Boolean satisfiability problem, we find effective designs and selectively suppress unwanted structures.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(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
Nanoscience & Nanotechnology
Mathias Centola, Erik Poppleton, Sujay Ray, Martin Centola, Robb Welty, Julian Valero, Nils G. Walter, Petr Sulc, Michael Famulok
Summary: Molecular engineering aims to design nanoassemblies for complex tasks, but efficient chemical-fuel-driven nanoscale driver-follower systems have not been realized. In this study, a DNA nanomachine driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates was developed, generating rhythmic pulsating motion and successfully coupling with a passive follower.
NATURE NANOTECHNOLOGY
(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)
