Article
Meteorology & Atmospheric Sciences
Stuart Patching
Summary: This article explores the problem of coarse-graining in finite-volume fluid models and proposes a method for choosing averaging weights to preserve divergence and gradient. Specific values for the averaging weights are found for a regular triangular mesh with B-grid variable placement. It is also observed that the same coarse-graining method that preserves divergence also preserves the vertical component of the curl.
Article
Biochemistry & Molecular Biology
Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, Agnieszka G. Lipska, Sergey A. Samsonov, Rajesh K. Murarka
Summary: This review article discusses the physical basis, force fields, equations of motion, numerical integration algorithms, and applications of coarse-grained molecular dynamics. By integrating out secondary degrees of freedom, the motion of coarse-grained sites is controlled, leading to simulations at a coarse-grained level.
Article
Multidisciplinary Sciences
Brecht Donvil, Paolo Muratore-Ginanneschi
Summary: This research proves that general time-local and trace-preserving master equations can also be unraveled into a Markov process in the Hilbert space of the system by weighing averages with a probability pseudo-measure called the influence martingale. In addition, the authors introduce a quantum trajectory framework for time local master equations derived at strong coupling by including an extra 1D variable in the dynamics while keeping the computational complexity under control.
NATURE COMMUNICATIONS
(2022)
Article
Polymer Science
Ting Ge, Jiuling Wang, Mark O. Robbins
Summary: As the degree of coarse-graining increases, the stress level during strain hardening decreases, but the stress-strain curves can be collapsed with a simple rescaling factor. In the same strain range, the conformational changes in local chain segments are almost the same.
Article
Computer Science, Interdisciplinary Applications
Joseph Bakarji, Daniel M. Tartakovsky
Summary: Statistical (machine learning) tools for equation discovery require large amounts of data, typically computer generated rather than experimentally observed. Learning on simulated data in areas such as multiscale modeling and stochastic simulations can lead to discovery. Our machine-learning strategy based on sparse regression replaces human discovery of models and can be executed in two modes.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Article
Physics, Fluids & Plasmas
Pierpaolo Bilotto, Lorenzo Caprini, Angelo Vulpiani
Summary: This study investigates the effect of coarse graining on the thermodynamic properties of a system by considering a one-dimensional colloidal particle in a sinusoidal potential driven out of equilibrium. Different levels of coarse graining were evaluated, revealing the impact of friction values on entropy production and the influence of inertia on jump statistics and average jump rate. The periodic shape of the potential allowed for the approximation of continuous dynamics via a Markov chain after introducing suitable time and space discretization.
Article
Mathematics, Applied
Matthias Klar, Karsten Matthies, Celia Reina, Johannes Zimmer
Summary: This study explores a class of fast-slow Hamiltonian systems describing the interaction of non-ergodic fast and slow degrees of freedom, focusing on the situation where epsilon is small but positive. It rigorously derives second-order corrections to the homogenised degrees of freedom and analyses the energy of the fast degrees expanded to second-order from a thermodynamic perspective, showing that they satisfy thermodynamic energy relations akin to the laws of thermodynamics. Additionally, a numerical analysis is conducted on the second-order asymptotic expansion of the slow degrees of freedom for a specific system, comparing their approximation quality and total computation time with the original solution.
PHYSICA D-NONLINEAR PHENOMENA
(2021)
Article
Chemistry, Physical
Pietro Corsi, Alvaro Gonzalez Garcia, Elia Roma, Tecla Gasperi, Barbara Capone
Summary: In this study, adsorption properties in bottlebrush/colloid binary mixtures were investigated using scaling theories, theoretical predictions, SCFC, and molecular dynamics simulations. The onset of adsorption was found to be influenced by the local properties of the adsorbing guest particle, which could be predicted using simple scaling arguments. Validation of predictions was done through molecular dynamics simulations, paving the way for smart rational design and coarse-graining of adsorbing/releasing systems.
Article
Polymer Science
Kevin R. Hinkle
Summary: Molecular dynamics simulations were used to verify the accuracy of using coarse-grained models to describe diblock-arm star polymers. The results showed agreement with atomistic models, reproduced general trends, and investigated structure-property relationships by varying arm number and length. This work is an important first step towards improved design of polymeric nanoparticles for drug delivery applications.
EUROPEAN POLYMER JOURNAL
(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
Quantum Science & Technology
Xiang Zhou
Summary: This paper presents a superposition measure with respect to coarse-grained measurement. The initial state used is a special kind of mixed state called the generalized n-qubit Werner state. By applying an appropriate coarse-graining to the initial state, it is found that the observational entropy and the von Neumann entropy are equal for any n. Furthermore, the difference between observational entropy and von Neumann entropy is studied for another coarse-graining, and it is found to satisfy the condition of superposition measure, indicating it can be regarded as a superposition measure with respect to a coarse-grained measurement. The characterizations of this superposition measure are investigated.
QUANTUM INFORMATION PROCESSING
(2023)
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)
Article
Chemistry, Physical
Mamta Yadav, Yashwant Singh
Summary: We have developed a theory to trace the solvent degrees of freedom in colloid-solvent mixtures based on the grand partition function. Our approach uses density functional formalism and considers the solvent-induced interactions expressed in terms of two functionals. The theory provides insights into the nature of the potential and its dependence on thermodynamic state, packing fractions, and size ratio. We applied the theory to additive and nonadditive binary hard-sphere mixtures and observed interesting features such as non-monotonic dependence of the attractive part of the potential on the packing fraction.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Review
Chemistry, Multidisciplinary
Rui Shi, Hu-Jun Qian, Zhong-Yuan Lu
Summary: Coarse-grained (CG) molecular dynamics simulations are important for the simulations of polymeric systems due to their computational efficiency and ability to provide structural and dynamical properties. CG models have been developed in two directions: generic models focusing on capturing general properties, and chemically-specific models retaining chemical-physical properties. However, faithfully reproducing structure and dynamics is a major challenge due to the reduction of atomistic degree of freedom. This review provides an overview of recent achievements and remaining challenges in the development of chemically-specific CG approaches for polymer systems simulations.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Editorial Material
Neurosciences
Kerstin Preuschoff
Summary: The study reveals two parallel valuation mechanisms by investigating the value signals of caudate nucleus and orbitofrontal cortex during choice.
Article
Biochemistry & Molecular Biology
Thomas Bourguignon, Yukihiro Kinjo, Paula Villa-Martin, Nicholas V. Coleman, Qian Tang, Daej A. Arab, Zongqing Wang, Gaku Tokuda, Yuichi Hongoh, Moriya Ohkuma, Simon Y. W. Ho, Simone Pigolotti, Nathan Lo
Article
Mechanics
John Bechhoefer, Sergio Ciliberto, Simone Pigolotti, Edgar Roldan
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2020)
Article
Multidisciplinary Sciences
Paula Villa Martin, Ales Bucek, Tomas Bourguignon, Simone Pigolotti
Article
Multidisciplinary Sciences
Xingbo Yang, Matthias Heinemann, Jonathon Howard, Greg Huber, Srividya Iyer-Biswas, Guillaume Le Treut, Michael Lynch, Kristi L. Montooth, Daniel J. Needleman, Simone Pigolotti, Jonathan Rodenfels, Pierre Ronceray, Sadasivan Shankar, Iman Tavassoly, Shashi Thutupalli, Denis Titov, Jin Wang, Peter J. Foster
Summary: Cells, as the basic units of living matter, utilize energy to drive life processes. Physical bioenergetics aims to understand the energy usage, allocation, and constraints in cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Physics, Multidisciplinary
Jose M. Miotto, Simone Pigolotti, Aleksei Chechkin, Sandalo Roldan-Vargas
Summary: This study reveals the existence of Brownian yet non-Gaussian regimes in mesoscopic particle systems, contrary to classical theory, and proposes a new scaling theory to explain this phenomenon. Simulations show different scaling behaviors of the length scale λ in different systems, suggesting a link between this phenomenon and glassy dynamics.
Article
Physics, Multidisciplinary
Qiao Lu, Deepak Bhat, Darya Stepanenko, Simone Pigolotti
Summary: The CRISPR-Cas9 system is an important gene editing tool where the key component Cas9 can search for and cleave specific target sequences on the DNA through sliding. Studies have shown that the sliding length of Cas9 is short, and the distribution of Cas9 molecules along the DNA can be rationalized through the theory of Anderson localization.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Anzhelika Koldaeva, Hsieh-Fu Tsai, Amy Q. Shen, Simone Pigolotti
Summary: This study investigates the population genetics of Escherichia coli proliferating in microchannels, revealing that diversity is rapidly lost within channels but much slower among them. Competitive E. coli strains must organize into an ordered stripe pattern in a few generations. Random mutations in the middle of the channel are more likely to become fixed, illustrating fundamental mechanisms of microbial evolution in spatially confined environments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Analytical
Hsieh-Fu Tsai, Daniel W. Carlson, Anzhelika Koldaeva, Simone Pigolotti, Amy Q. Shen
Summary: In this work, an integrated and hydrodynamically-optimized microfluidic chip was designed and fabricated to study the long-term dynamics of Escherichia coli populations in confined microchannels. By using a microscopy immersion oil with stable viscosity, successful time-lapse imaging of the bacteria was achieved for more than 72 hours. This fabrication and imaging methodology could be applicable to other single-cell studies that require long-term imaging.
Article
Biology
Deepak Bhat, Samuel Hauf, Charles Plessy, Yohei Yokobayashi, Simone Pigolotti, Armita Nourmohammad
Summary: In this study, a new method was proposed to infer the dynamics of Replisomes from DNA abundance distribution. The method was applied to measure the DNA abundance distribution in Escherichia coli populations growing at different temperatures. The results showed that the speed of Replisomes increases with temperature and exhibits wave-like variations along the genome, which correlates with the variation of mutation rate. This study provides insights into the replication dynamics of bacteria.
Article
Physics, Multidisciplinary
Davide Chiuchiu, Shrabani Mondal, Simone Pigolotti
Summary: Biological processes such as DNA replication, RNA transcription, and protein translation achieve speed and accuracy by dissipating chemical energy in non-equilibrium reactions. These systems involve a trade-off between speed, error, and dissipation. This paper quantifies this trade-off using mathematical optimization theory and characterizes the Pareto optimal front for a generalized kinetic proofreading model. The findings suggest that models with more proofreading steps exhibit better trade-offs and reveal scaling relations between speed, accuracy, and dissipation on the Pareto front.
NEW JOURNAL OF PHYSICS
(2023)
Article
Physics, Fluids & Plasmas
Paula Villa Martin, Anzhelika Koldaeva, Simone Pigolotti
Summary: This paper introduces a spatial coalescence model to study the diversity of planktonic communities. By simulating a small number of individuals instead of the entire community, this approach is more time-saving and efficient compared to individual-based models.
Article
Biochemistry & Molecular Biology
Yukihiro Kinjo, Nathan Lo, Paula Villa Martin, Gaku Tokuda, Simone Pigolotti, Thomas Bourguignon
Summary: This study identified three mechanisms leading to gene loss in the intracellular endosymbiont Blattabacterium: gene loss rates increase exponentially with the accumulation of substitutions, genes involved in vitamin and amino acid metabolism undergo relaxed selection in certain lineages, and interactions among genes result in a domino effect of gene loss within pathways.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Physics, Fluids & Plasmas
Simone Pigolotti
Summary: The study investigates the fluctuation of cell division times in microbial populations and finds that population growth is significantly impacted. Depending on whether fluctuations are correlated among different cells, either the Euler-Lotka equation or a similar equation that accounts for correlations is used to predict population growth rates.
Article
Physics, Multidisciplinary
Simone Pigolotti, Mogens H. Jensen, Yinxiu Zhan, Guido Tiana
PHYSICAL REVIEW RESEARCH
(2020)
Meeting Abstract
Biophysics
Davide Chiuchiu, Yuhai Tu, Simone Pigolotti
BIOPHYSICAL JOURNAL
(2020)
