Article
Chemistry, Physical
Tiedong Sun, Vishal Minhas, Alexander Mirzoev, Nikolay Korolev, Alexander P. Lyubartsev, Lars Nordenskiold
Summary: Researchers have developed a coarse-grained model of the nucleosome core particle (NCP) using a systematic bottom-up approach. The model accurately reproduces the known structural features of the NCP and provides a realistic description of nucleosome-nucleosome attraction in the presence of multivalent cations. This model opens up possibilities for rigorous modeling of chromatin fibers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
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)
Article
Chemistry, Physical
Gaurav Chauhan, Michael L. Simpson, Steven M. Abel
Summary: Macromolecular crowding in cellular and cell-free systems can affect the interactions of semiflexible biopolymers with surfaces. The adsorption of semiflexible polymers on repulsive surfaces is promoted by stiffer polymers, smaller crowding particles, and larger volume fractions of crowders. Crowding-induced transitions from non-adsorbed to partially and strongly adsorbed states occur at smaller values of bending stiffness as the volume fraction of crowders increases.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Ainara Claveras Cabezudo, Christina Athanasiou, Alexandros Tsengenes, Rebecca C. Wade
Summary: Reducing the nonbonded interactions between protein and water enables protein encapsulation in phospholipid micelles and bilayers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Hiram Isaac Beltran, Salomon J. Alas-Guardado, Pedro Pablo Gonzalez-Perez
Summary: In this study, the folding of 7 hydrophobic-polar sequences in two types of 2D-square space lattices, homogeneous and correlated, was tested. It was found that using correlated networks led to more successful structural trials compared to a homogeneous lattice. The majority of the sequences were designed by the researchers, and the goal of the study was to obtain a modified 2D HP lattice model that mimics protein folding in crowded environments. The results showed that folding sequences in crowded spaces achieved better results than in homogeneous ones.
JOURNAL OF MOLECULAR MODELING
(2022)
Article
Quantum Science & Technology
Karen Hovhannisyan, Mathias R. Jorgensen, Gabriel T. Landi, Alvaro M. Alhambra, Jonatan B. Brask, Marti Perarnau-Llobet
Summary: Accurate thermometry for quantum systems is crucial for technological advancement, but practical implementations often involve coarse-grained measurements. By utilizing tools from signal processing, we can achieve good temperature estimates even with a small number of outcomes. Our findings have implications for many-body systems and nonequilibrium thermometry, providing insights into optimal coarse-grained measurements and strategies for probe-based thermometry.
Article
Physics, Fluids & Plasmas
Fane Feng, Ting Lei, Nanrong Zhao
Summary: The study uses two-dimensional Langevin dynamics simulations to investigate the effective interactions between passive colloids in a bath with active particles. The results show that factors such as active particle size, crowding-activity coupling, and chirality have significant effects on the attraction or repulsion between particles. As volume fraction increases, the competition between activity and crowding leads to a transition from repulsion to attraction in the effective force.
Article
Optics
Lewis W. Anderson, Martin Kiffner, Panagiotis Kl. Barkoutsos, Ivano Tavernelli, Jason Crain, Dieter Jaksch
Summary: The study develops a coarse-grained representation of electronic response suitable for determining the ground state of weakly interacting molecules using VQA, demonstrating its capability on IBM superconducting quantum processors and showing potential for probing energies in weakly bound regimes.
Article
Polymer Science
Juan J. de Pablo, Heyi Liang, Michael A. Webb, Manasi Chawathe, Denis Bendejacq
Summary: Understanding and predicting the behavior of galactomannans in aqueous solutions is important for various applications. In this study, a coarse-grained model of guar gum, a type of galactomannan, was developed and validated. The model showed good agreement with experimental results in terms of chain structure, aggregate formation, and solution viscosity. The behavior of guar gum in water was explained using scaling theory for polymers in good solvents.
Article
Chemistry, Multidisciplinary
Sarah Wettermann, Ranajay Datta, Peter Virnau
Summary: We investigate the probability of knotting in long double-stranded DNA strands using a coarse-grained Kratky-Porod model and Monte Carlo simulations. We manipulate the ionic conditions by adjusting the effective diameter of monomers. Our findings show that high salt conditions and confinement between plates significantly increase the occurrence of knots, while knots can be almost completely dissolved in low salt scenarios. Comparisons with recent experiments indicate that the coarse-grained model accurately captures and predicts topological features of DNA, making it a useful tool for guiding future experiments on DNA knots.
FRONTIERS IN CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Robert Zando, Mauro Chinappi, Cristiano Giordani, Fabio Cecconi, Zhen Zhang
Summary: Nanopores and nanocavities are potential tools for studying individual molecules in confined spaces. The dwell time of an analyte in a nanocavity with nanopore gates depends on their sizes and particle-wall interactions. Increasing particle-wall attraction transforms the diffusion process from 3D to 2D motion, resulting in a significant reduction of the average dwell time. Comparison with existing theories allows for quantifying the reliability of ideal condition-derived theories for actual device geometries.
Article
Chemistry, Physical
Srdjan Pusara, Peyman Yamin, Wolfgang Wenzel, Marjan Krstic, Mariana Kozlowska
Summary: Colloidal protein-protein interactions play a crucial role in biotechnological processes, but are complex and difficult to understand through measurements alone. The osmotic second virial coefficient, B-22, can be used to estimate these interactions in diluted protein solutions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Robotics
Aamodh Suresh, Angelique Taylor, Laurel D. D. Riek, Sonia Martinez
Summary: This research aims to understand human preferences and behaviors in risky and crowded environments, specifically in navigational settings. The study shows that individuals have diverse path preferences ranging from risky and urgent to safe and relaxed. It also reveals that self-assessed risk and time-urgency do not correlate with path preferences. Additionally, participants express a high interest in understanding robot intentions and decision-making through various modalities like speech, touchscreen, and gestures. These findings provide crucial insights for the design of explainable AI in robots deployed in risky and crowded environments.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2023)
Article
Chemistry, Medicinal
Xiaorong Liu, Jianhan Chen, Yumeng Zhang
Summary: Intrinsically disordered proteins (IDPs) play crucial roles in cellular regulatory networks. The HyRes II model can semi-quantitatively reproduce the structural properties of IDPs and simulate their dynamic interactions efficiently.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
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
Biochemistry & Molecular Biology
Kamaludin Dingle, Fatme Ghaddar, Petr Sulc, Ard A. Louis
Summary: Developmental bias is the primary explanation for the occupation of the RNA secondary structure morphospace, with only the most frequent structures appearing in nature and a small number of random sequences needed to produce all observed RNA secondary structures. These patterns are accurately predicted by the likelihood of structures appearing upon a uniform random sampling of sequences.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Physics, Condensed Matter
John Russo, Flavio Romano, Lukas Kroc, Francesco Sciortino, Lorenzo Rovigatti, Petr Sulc
Summary: This study proposes a general framework for solving inverse self-assembly problems and successfully demonstrates the design and numerical simulation of a specific cubic diamond structure. The approach uses patchy particles as building blocks and transforms the problem into a Boolean satisfiability problem to determine the interaction rules between patches.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2022)
Article
Biochemistry & Molecular Biology
Erik Poppleton, Aatmik Mallya, Swarup Dey, Joel Joseph, Petr Sulc
Summary: The database is an online resource for nucleic acid nanostructures, providing an upload interface, searching and database browsing capabilities. It includes conversion tools to encourage design file conversion, aiming to facilitate sharing and reuse of designs in the DNA/RNA nanotechnology community.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Chad R. Simmons, Tara MacCulloch, Miroslav Krepl, Michael Matthies, Alex Buchberger, Ilyssa Crawford, Jiri Sponer, Petr Sulc, Nicholas Stephanopoulos, Hao Yan
Summary: Engineered crystal architectures from DNA have become a foundational goal for nanotechnological precise arrangement. Here, the authors systematically investigate the structures of 36 immobile Holliday junction sequences and identify the features allowing the crystallisation of most of them, while 6 are considered fatal.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Lan Liu, Fan Hong, Hao Liu, Xu Zhou, Shuoxing Jiang, Petr Sulc, Jian-Hui Jiang, Hao Yan
Summary: The identity and timing of environmental stimulus are crucial for signaling networks and phenotypic development in living organisms. A DNA finite-state machine has been developed to sense and record temporally ordered inputs, showing potential for time-resolved biosensing and smart therapeutics.
Review
Biochemical Research Methods
Joakim Bohlin, Michael Matthies, Erik Poppleton, Jonah Procyk, Aatmik Mallya, Hao Yan, Petr Sulc
Summary: Molecular simulation is essential in DNA/RNA nanotechnology research, improving the precision of nanoscaffolds and diagnostic tools. oxView is a design tool for visualizing, designing, editing, and analyzing simulations of DNA, RNA, and nucleic acid-protein nanostructures, providing an accessible software platform for researchers to integrate simulation and 3D visualization into their projects.
Article
Biochemical Research Methods
Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S. Schreck, Yu Zhou, Yan Liu, Remi Monasson, Simona Cocco, Petr Sulc
Summary: In this study, Restricted Boltzmann Machines (RBMs) were successfully trained on sequence ensembles from SELEX experiments to predict the effects of selection and generate novel aptamers with potential disruptive mutations or good binding properties.
PLOS COMPUTATIONAL BIOLOGY
(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, 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, 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
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
Chemistry, Multidisciplinary
Lorenzo Rovigatti, John Russo, Flavio Romano, Michael Matthies, Lukas Kroc, Petr Sulc
Summary: In this study, we address the problems faced during the self-assembly of colloidal diamond crystals by using the SAT-assembly design framework. We demonstrate that the assembly of CD crystals only requires a binary mixture, and we test a promising DNA nanotechnology design using molecular dynamics simulations.
