Article
Multidisciplinary Sciences
Pauline Formaglio, Marina E. Wosniack, Raphael M. Tromer, Jaderson G. Polli, Yuri B. Matos, Hang Zhong, Ernesto P. Raposo, Marcos G. E. da Luz, Rogerio Amino
Summary: Plasmodium sporozoites actively migrate in the dermis and enter blood vessels to induce infection. Through intravital imaging, researchers found that sporozoites adopt a strategy of alternating global superdiffusive skin exploration and local subdiffusive blood vessel exploitation, enabling them to find intravasation hotspots associated with pericytes, enter the bloodstream and initiate malaria infection.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Ran Liu, Xiang Liu, Jie Wu
Summary: In this study, we propose molecular descriptors based on persistent path-spectral and a machine learning model based on persistent path-spectral for the prediction of protein-ligand binding affinity. Our model combines the molecular descriptors from persistent path-spectral attributes with the gradient boosting tree machine learning model. We test this model on three commonly used datasets and achieve competitive results.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Physics, Fluids & Plasmas
Fernanda H. Gonzalez, Alejandro P. Riascos, Denis Boyer
Summary: The study focuses on diffusive transport of Markovian random walks on networks with stochastic resetting to multiple nodes. Analytical expressions for stationary occupation probability, mean, and global first passage times are derived to characterize the effect of resetting on random walk strategies. The methods are applied to various dynamics, including Levy flights and Google random walk strategy.
Article
Physics, Fluids & Plasmas
Fei Ma, Ping Wang
Summary: The study proposes a simple algorithmic framework for generating power-law graphs with small diameters and examines their structural properties. The results show that these graphs have unique features such as density characteristics and higher trapping efficiency compared to existing scale-free models, confirmed through extensive simulations.
Article
Physics, Mathematical
Wai-Tong Louis Fan, Wenqing Hu, Grigory Terlov
Summary: This study analyzes the asymptotic wave speed for FKPP type reaction-diffusion equations on a class of infinite random metric trees, demonstrating the emergence of a traveling wavefront when the reaction rate is sufficiently large. The wavefront speed is quantified using a variational formula involving random branching degrees and random branch lengths. This speed is slower than that of the same equation on the real line, with estimates in terms of the tree's metric structure. The analysis connects wavefront propagation to the large deviations principle of multi-skewed Brownian motion with random parameters, involving delicate estimates for random matrices and hitting times of a random walk in a random environment.
COMMUNICATIONS IN MATHEMATICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Alexandre Bovet, Jean-Charles Delvenne, Renaud Lambiotte
Summary: This article introduces a method based on a dynamical process evolving on a temporal network, which uncovers different dynamic scales in a system by considering the ordering of edges in forward and backward time. The method provides a new approach to extracting a simplified view of time-dependent network interactions in a system.
Article
Astronomy & Astrophysics
Anh Dung Le, Alfred H. Mueller, Stephane Munier
Summary: This study examines the scattering of a small onium off a large nucleus at high center-of-mass energies, using the color dipole picture in quantum chromodynamics. By analyzing different reference frames, it is shown that complete asymptotic expressions can be derived beyond the total cross section, based on limited knowledge of the Balitsky-Kovchegov equation solutions. An analytic expression for the rapidity distribution of the first branching of the slowest parent dipole is obtained, which provides an estimator of the correlations of interacting dipoles and is relevant to diffractive dissociation phenomena. The results presented may have broader implications for one-dimensional branching random walk models.
Article
Physics, Fluids & Plasmas
Federica Baccini, Filippo Geraci, Ginestra Bianconi
Summary: This study addresses the limitations of unweighted simplical complexes in representing higher-order interactions by introducing weighted simplical complexes, which can capture the weighted topology of the data without information loss.
Article
Physics, Fluids & Plasmas
J. Cleland, M. A. K. Williams
Summary: This article explores the mathematical description of anomalous diffusion driven by internal stresses instead of thermal fluctuations. It outlines a continuous time random walk framework to describe the waiting times between displacements, and identifies the associated generalized diffusion equation. The probability density function and second moment display different characteristics at different timescales, transitioning between subdiffusive and diffusive behavior.
Article
Physics, Fluids & Plasmas
Costantino Di Bello, Alexander K. Hartmann, Satya N. Majumdar, Francesco Mori, Alberto Rosso, Gregory Schehr
Summary: This article investigates the effects of resetting on the distribution of the integrated particle current in a system of noninteracting particles on a line. Two different models, namely independent Brownian motion with resetting and run-and-tumble motion with resetting, are considered. The study shows that resetting induces a stationary limiting distribution of the current at long times, but the approach to the stationary state is drastically different for annealed and quenched cases. A third-order phase transition is observed in the rate function of the quenched distribution. Numerical and analytical methods are used to compute the associated rate functions for both models.
Article
Mathematics, Applied
Zhenhua Yuan, Yongjin Chen, Long Gao, Junhao Peng
Summary: This study investigates the first encounters between two particles in Watts-Strogatz networks and Barabasi-Albert networks. The results show that the impact of prey's motion on encounter time differs between the two networks, and different initial conditions can also affect the results.
Article
Mathematics, Applied
Hui Fu, Guo-Cheng Wu, Guang Yang, Lan-Lan Huang
Summary: This study revisits the standard definition of the Riemann-Liouville integral and introduces a new fractional integral with an exponential kernel. It provides some useful properties such as the composition relationship of the new fractional integral and Leibniz integral law. Additionally, exact solutions for the fractional homogeneous equation and non-homogeneous equations are given, along with a finite difference scheme for solving fractional nonlinear differential equations with exponential memory, demonstrating the efficiency and convenience of the new fractional derivative.
Article
Statistics & Probability
Philip A. Ernst, Dongzhou Huang, Frederi G. Viens
Summary: This paper provides an exact formula for the second moment of the empirical correlation for two independent standard Gaussian random walks, as well as implicit formulas for higher moments. It also establishes rates of convergence of the empirical correlation of two independent standard Gaussian random walks to the empirical correlation of two independent Wiener processes.
STOCHASTIC PROCESSES AND THEIR APPLICATIONS
(2023)
Article
Physics, Multidisciplinary
Naftali R. Smith, Satya N. Majumdar, Gregory Schehr
Summary: This study investigates a random process x(tau) that undergoes stochastic resetting at a constant rate r with a position chosen from a distribution P(x). The study considers a sequence of dynamical observables A1, ..., An related to the intervals between resetting events. The study calculates the exact probabilities of various events associated with this sequence, such as the last element being larger than all previous ones, or the sequence being monotonically increasing. Remarkably, the study finds that these probabilities are super-universal, meaning they are independent of the specific process x(tau), the observables Ak's, and the resetting distribution P(x). The universality holds for some events as long as certain mild assumptions on the process and observables are met, such as mirror symmetry.
Article
Physics, Multidisciplinary
L. Regnier, O. Benichou, P. L. Krapivsky
Summary: We introduce range-controlled random walks with hopping rates depending on the range N, that is, the total number of previously distinct visited sites. We analyze a one-parameter class of models with a hopping rate Na and determine the large time behavior of the average range, as well as its complete distribution in two limit cases. We find that the behavior drastically changes depending on whether the exponent a is smaller, equal, or larger than the critical value, ad, depending only on the spatial dimension d.
PHYSICAL REVIEW LETTERS
(2023)
Article
Multidisciplinary Sciences
Daniel S. Seara, Benjamin B. Machta, Michael P. Murrell
Summary: Recent research has shown that living and non-living active matter consume energy at the microscopic scale to drive macroscopic behavior. Introducing a measure of irreversibility, termed the entropy production factor, can quantify how time reversal symmetry is broken in field theories and characterize dynamical phase transitions in systems. This method can help in analyzing the energetic cost and distribution of irreversibility in spatiotemporal frequencies across different scales.
NATURE COMMUNICATIONS
(2021)
Article
Mathematics, Applied
Re'em Harel, Stanislav Burov, Shay I. Heizler
Summary: The study examines the validity of the time-dependent asymptotic P-N approximation in radiative transfer of photons, showing that this method yields excellent results in controlling the particle velocity that determines the radiative heat-wave fronts.
JOURNAL OF COMPUTATIONAL AND THEORETICAL TRANSPORT
(2021)
Article
Physics, Multidisciplinary
M. Hidalgo-Soria, E. Barkai, S. Burov
Summary: In a study of a two state jumping diffusivity model for a Brownian process, it was found that Gaussian behavior is recovered in the long measurement times, while short time behavior leads to a non-analytic cusp-like shape in the distribution of displacements. This cusp-like behavior resembles that found in experiments of diffusing particles in disordered environments, and it depends on the existence of finite mean values of waiting times at different states of the model.
Article
Nuclear Science & Technology
Re'em Harel, Stanislav Burov, Shay I. Heizler
Summary: The study introduces a spatio-temporal approach for solving the time-dependent Boltzmann equation, providing a more accurate solution compared to the classical P-N approximation, especially in highly anisotropic problems. Additionally, the proposed approximation demonstrates faster convergence in benchmark testing against the full Green function in infinite media.
NUCLEAR SCIENCE AND ENGINEERING
(2021)
Article
Physics, Multidisciplinary
M. S. Yousafzai, V Yadav, S. Amiri, Y. Errami, S. Amiri, M. Murrell
Summary: This study explores the relationship between the nonequilibrium generation of myosin-induced active stress and the pressure-volume relationship of cellular aggregates. It is found that the aggregate surface tension and cell number density depend on size, violating equilibrium assumptions. However, the relationship between them resembles an equilibrium equation of state with an effective temperature.
PHYSICAL REVIEW LETTERS
(2022)
Article
Physics, Fluids & Plasmas
Vikrant Yadav, Md Sulaiman Yousafzai, Sorosh Amiri, Robert W. Style, Eric R. Dufresne, Michael Murrell
Summary: The surface tension of living cells and tissues originates from the generation of nonequilibrium active stresses within the cell cytoskeleton. Gradients in the surface tension can drive large-scale and rapid toroidal motion in cellular aggregates. These motions resemble Marangoni flows in viscous fluids and are dependent on the volume of the aggregate.
PHYSICAL REVIEW FLUIDS
(2022)
Article
Physics, Multidisciplinary
Muhammad Sulaiman Yousafzai, Vikrant Yadav, Sorosh Amiri, Michael F. Staddon, Youssef Errami, Gwilherm Jaspard, Shiladitya Banerjee, Michael Murrell
Summary: The magnitude of mechanical stresses caused by cell surface tension may be comparable to the bulk elasticity of their matrix on cellular length scales, but the influence of capillary effects on tissue shape and motion is still unclear. In this study, wetting of cell aggregates on adhesive substrates of varying elasticity was induced to investigate the dynamics of wetting and the balance of interfacial tensions. The results showed that myosin-driven active elastocapillary effects enable the adaptation of wetting mechanisms to substrate rigidity and introduce a novel, pressure-based mechanism for guiding collective cell motion.
Article
Biochemistry & Molecular Biology
Sung Hoon Lee, Jay C. Hou, Archer Hamidzadeh, M. Sulaiman Yousafzai, Visar Ajeti, Hao Chang, David J. Odde, Michael Murrell, Andre Levchenko
Summary: This study reveals that cyclic changes in the activity of the small GTPase RhoA, mediated by the RhoA guanine nucleotide exchange factor GEF-H1 and triggered by an increase in intracellular Ca2+ levels, are responsible for navigation through a dense extracellular matrix during cell migration. The cyclic changes are driven by two coupled negative feedback loops dependent on microtubule dynamics. Additionally, an increasing frequency of the molecular clock leads to faster cell migration within physically confining spaces.
Article
Multidisciplinary Sciences
Camelia G. Muresan, Zachary Gao Sun, Vikrant Yadav, A. Pasha Tabatabai, Laura Lanier, June Hyung Kim, Taeyoon Kim, Michael P. Murrell
Summary: This study shows that the different architectures of F-actin have distinct effects on stress generation and transmission, which play important roles in the essential behaviors of cells.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Hao Xing, Yaqing Huang, Britta H. Kunkemoeller, Peter J. Dahl, Ohvia Muraleetharan, Nikhil S. Malvankar, Michael P. Murrell, Themis R. Kyriakides
Summary: Fibroblasts in diabetes show altered morphology, migration, extracellular matrix production, traction force, 3D contraction, and cell stiffness, which are associated with decreased active Rac1 and lack of co-localization between F-actin and WAVE2. Deletion of thrombospondin-2 rescues these phenotypes and restores normal levels of active Rac1 and WAVE2-F-actin co-localization.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Ryota Sakamoto, Deb Sankar Banerjee, Vikrant Yadav, Sheng Chen, Margaret Gardel, Cecile Sykes, Shiladitya Banerjee, Michael P. Murrell
Summary: The accumulation and transmission of mechanical stresses in the cell cortex and membrane determine the mechanics of cell shape and coordinate essential physical behaviors. The relative roles of the membrane and cytoskeleton in the transmission of mechanical stresses for diverse behaviors are unclear.
COMMUNICATIONS BIOLOGY
(2023)
Correction
Biology
Ryota Sakamoto, Deb Sankar Banerjee, Vikrant Yadav, Sheng Chen, Margaret L. Gardel, Cecile Sykes, Shiladitya Banerjee, Michael P. Murrell
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Physical
Michael F. Staddon, Michael P. Murrell, Shiladitya Banerjee
Summary: The coordinated and cooperative motion of cells plays a crucial role in embryonic development, tissue morphogenesis, wound healing, and cancer invasion. By developing a predictive cellular vertex model, we can understand the relative roles of substrate rigidity, tissue mechanics, and active cell properties in collective cell motion. Our model predicts that the cooperation of cell crawling and tissue pressure drives faster spreading, with the spreading rate being sensitive to the mechanical properties of the tissue.
Article
Physics, Fluids & Plasmas
Deborah Schwarcz, Stanislav Burov
Summary: Recent experiments have shown that using a liquid substrate can improve the production of amorphous materials. Our study demonstrates that introducing motion to the substrate atoms can enhance the self-assembly process of particles on top of the substrate.
Article
Materials Science, Multidisciplinary
L. Burlachkov, S. Burov
Summary: In type II superconductors, the attraction and annihilation of Abrikosov vortices with different polarities at B = 0 lines result in the redistribution of magnetization current over the sample, slowing down the rate of magnetic relaxation. This effect is most pronounced in the remanent state, especially for flux flow and early stages of flux creep.
