Physical Review EPub Date : 2025-02-01DOI: 10.1103/PhysRevE.111.024408
Duncan Kirby, Anton Zilman
{"title":"Ligand-induced receptor multimerization achieves specificity enhancement of kinetic proofreading without associated costs.","authors":"Duncan Kirby, Anton Zilman","doi":"10.1103/PhysRevE.111.024408","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024408","url":null,"abstract":"<p><p>Kinetic proofreading (KPR) is a commonly invoked mechanism for specificity enhancement of receptor signaling. However, specificity enhancement comes at a cost of nonequilibrium energy input and signal attenuation. We show that ligand-induced multimeric receptor assembly can enhance receptor specificity to the same degree as KPR, yet without the need for out-of-equilibrium energy expenditure and signal loss. We show how multimeric receptor specificity enhancement arises from the amplification of affinity differences via sequential progression down a free energy landscape. We also show that multimeric receptor ligand recognition is more robust to stochastic fluctuations and molecular noise than KPR receptors. Finally, we show that multimeric receptors perform signaling tasks beyond specificity enhancement like absolute discrimination and aspects of ligand antagonism. Our results suggest that multimeric receptors may serve as a potent mechanism of ligand discrimination comparable to and potentially with more advantages than traditional proofreading.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024408"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Physical Review EPub Date : 2025-02-01DOI: 10.1103/PhysRevE.111.L023302
D H G Duarte, P D S de Lima, J M de Araújo
{"title":"Outlier-resistant physics-informed neural network.","authors":"D H G Duarte, P D S de Lima, J M de Araújo","doi":"10.1103/PhysRevE.111.L023302","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.L023302","url":null,"abstract":"<p><p>Recent advances in machine learning have introduced physics-informed neural networks (PINN) as a valuable tool for addressing dynamics through governing equations and experimental observations. Outliers can be present in measurements and significantly affect the accuracy of the solutions provided by PINN. To overcome this limitation, we construct an outlier-resistant PINN (OrPINN) based on Tsallis statistics. We investigate the robustness of OrPINN in describing the acoustic and linear elastic wave dynamics under various outlier-level scenarios. We find that the OrPINN can improve the accuracy of the solutions even when the data is highly corrupted.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2","pages":"L023302"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Physical Review EPub Date : 2025-02-01DOI: 10.1103/PhysRevE.111.025415
O Martínez-Cano, J R Morillas, J Ruiz-Nievas, G Camacho, A Rodríguez-Barroso, J Ramírez, J de Vicente
{"title":"High-speed videomicroscopy and magnetorheology under triaxial unsteady magnetic fields.","authors":"O Martínez-Cano, J R Morillas, J Ruiz-Nievas, G Camacho, A Rodríguez-Barroso, J Ramírez, J de Vicente","doi":"10.1103/PhysRevE.111.025415","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.025415","url":null,"abstract":"<p><p>We describe a custom-built device that is capable of superimposing triaxial unsteady magnetic fields on a sample at the same time that its microstructure is visualized using a high-speed camera and its rheological properties are measured with a commercial rheometer. The device reaches field strengths up to 5 kA·m^{-1}, frequencies up to 4 kHz, and its functionality is evaluated by testing magnetorheological fluids under steady shear flow and field transients. Striking differences are found at small Mason numbers by changing the field configuration.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-2","pages":"025415"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Physical Review EPub Date : 2025-02-01DOI: 10.1103/PhysRevE.111.024116
Joonhyun Yeo, Haena Shim
{"title":"Structure of quantum mean force Gibbs states for coupled harmonic systems.","authors":"Joonhyun Yeo, Haena Shim","doi":"10.1103/PhysRevE.111.024116","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024116","url":null,"abstract":"<p><p>An open quantum system interacting with a heat bath at a given temperature is expected to reach the mean force Gibbs (MFG) state as a steady state. The MFG state is given by tracing out the bath degrees of freedom from the equilibrium Gibbs state of the total system plus bath. When the interaction between the system and the bath is not negligible, it is different from the usual system Gibbs state obtained from the system Hamiltonian only. Using the path integral method, we present the exact MFG state for a coupled system of quantum harmonic oscillators in contact with multiple thermal baths at the same temperature. We develop a nonperturbative method to calculate the covariances with respect to the MFG state. By comparing them with those obtained from the system Gibbs state, we find that the effect of coupling to the bath decays exponentially as a function of the distance from the system-bath boundary. This is similar to the skin effect found recently for a quantum spin chain interacting with an environment. Using the exact results, we also investigate the ultrastrong coupling limit where the coupling between the system and the bath gets arbitrarily large and makes a connection with the recent result found for a general quantum system.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024116"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Physical Review EPub Date : 2025-02-01DOI: 10.1103/PhysRevE.111.024127
J J Ruiz-Lorenzo, M Dudka, M Krasnytska, Yu Holovatch
{"title":"Emergence of the three-dimensional diluted Ising model universality class in a mixture of two magnets.","authors":"J J Ruiz-Lorenzo, M Dudka, M Krasnytska, Yu Holovatch","doi":"10.1103/PhysRevE.111.024127","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024127","url":null,"abstract":"<p><p>Usually, the impact of structural disorder on the magnetic phase transition in the 3D Ising model is analyzed within the framework of quenched dilution by a nonmagnetic component, where some lattice sites are occupied by Ising spins, while others are nonmagnetic. This kind of quenched dilution, according to the Harris criterion, leads to a change in the critical exponents that govern the asymptotics in the vicinity of the phase transition point. However, the inherent reason for the emergence of a new, random Ising model universality class is not the presence of a nonmagnetic component, but the disorder in structure of spin arrangement. To demonstrate this fact, in this paper we set up extensive Monte Carlo simulations of a random mixture of two Ising-like magnets that differ in spin length s and concentration c. In doing so, we analyze the effect of structural disorder per se without appealing to the presence of a nonmagnetic component. We support our numerical simulations with renormalization group calculations. Our results demonstrate the emergence of the 3D randomly diluted Ising model universality class in a random mixture of two Ising magnets. While the asymptotic critical exponents coincide with those known for the site-diluted 3D Ising model, the effective critical behavior is triggered by parameters s and c. The impact of their interplay is a subject of detailed analysis.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024127"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Physical Review EPub Date : 2025-02-01DOI: 10.1103/PhysRevE.111.024212
Juan C Vallejo, Alexandre R Nieto, Jesús M Seoane, Miguel A F Sanjuán
{"title":"Fast and slow escapes in forced chaotic scattering: The Newtonian and the relativistic regimes.","authors":"Juan C Vallejo, Alexandre R Nieto, Jesús M Seoane, Miguel A F Sanjuán","doi":"10.1103/PhysRevE.111.024212","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024212","url":null,"abstract":"<p><p>We study chaotic scattering phenomena in the paradigmatic Hénon-Heiles Hamiltonian when a rotating external force is applied. This analysis builds on and extends our previous work on the relativistic unperturbed case and the classical case with equal forcing terms affecting the equations of motion. In this more realistic scenario with a rotating external forcing, we compare the results obtained in the classical energy regime with those in the relativistic regime. Our comparison focuses on the analysis of the exit basins, as well as resonant and trapping phenomena, which correspond to fast and slow escape times, respectively. In addition to the dependence on the particle energy E, we also investigate the system's behavior at both low and high perturbing frequencies ω. Notably, when the particles are in the relativistic regime, we observe a shift in the evolution of the resonant frequency as a function of both E and ω.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024212"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Physical Review EPub Date : 2025-02-01DOI: 10.1103/PhysRevE.111.024126
Cheng Ma, Omar Malik, G Korniss
{"title":"Fluctuations and persistence in quantum diffusion on regular lattices.","authors":"Cheng Ma, Omar Malik, G Korniss","doi":"10.1103/PhysRevE.111.024126","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024126","url":null,"abstract":"<p><p>We investigate quantum persistence by analyzing amplitude and phase fluctuations of the wave function governed by the time-dependent free-particle Schrödinger equation. The quantum system is initialized with local random uncorrelated Gaussian amplitude and phase fluctuations. In analogy with classical diffusion, the persistence probability is defined as the probability that the local (amplitude or phase) fluctuations have not changed sign up to time t. Our results show that the persistence probability in quantum diffusion exhibits exponential-like tails. More specifically, in d=1 the persistence probability decays in a stretched exponential fashion, while in d=2 and d=3 as an exponential. We also provide some insights by analyzing the two-point spatial and temporal correlation functions in the limit of small fluctuations. In particular, in the long-time asymptotic limit, the temporal correlation functions for both local amplitude and phase fluctuations become time-homogeneous. Hence, the zero-crossing events correspond to those governed by a stationary Gaussian process, with an autocorrelation-function power-law tail decaying sufficiently fast to imply an exponential-like tail of the persistence probabilities.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024126"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Physical Review EPub Date : 2025-02-01DOI: 10.1103/PhysRevE.111.024136
Christopher N Angstmann, Daniel S Han, Bruce I Henry, Boris Z Huang, Zhuang Xu
{"title":"Compounded random walk for space-fractional diffusion on finite domains.","authors":"Christopher N Angstmann, Daniel S Han, Bruce I Henry, Boris Z Huang, Zhuang Xu","doi":"10.1103/PhysRevE.111.024136","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.024136","url":null,"abstract":"<p><p>We formulate a compounded random walk that is physically well defined on both finite and infinite domains, and samples space-dependent forces throughout jumps. The governing evolution equation for the walk limits to a space-fractional Fokker-Planck equation valid on bounded domains, and recovers the well known superdiffusive space-fractional diffusion equation on infinite domains. We describe methods for numerical approximation and Monte Carlo simulations and demonstrate excellent correspondence with analytical solutions. This compounded random walk, and its associated fractional Fokker-Planck equation, provides a major advance for modeling space-fractional diffusion through potential fields and on finite domains.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-1","pages":"024136"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Physical Review EPub Date : 2025-02-01DOI: 10.1103/PhysRevE.111.025503
Jacob M Diamond, K T Ramesh
{"title":"Spallation of polycarbonate on nanosecond timescales.","authors":"Jacob M Diamond, K T Ramesh","doi":"10.1103/PhysRevE.111.025503","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.025503","url":null,"abstract":"<p><p>Polycarbonate is commonly used in extreme environments, particularly in applications involving high-velocity impact. A critical failure mode in high-velocity impact is that of spallation, where intersecting release waves result in the dynamic fracture of the material under high-rate tension. Despite the ubiquity of polycarbonate, major gaps exist in our understanding of its behavior at high rates over very short timescales. Here we investigate the spallation of polycarbonate on nanosecond timescales at strain rates of ∼10^{6}s^{-1} through a data set of 117 spall experiments. The size and fidelity of our dataset allow us to calculate fundamental uncertainties associated with the spallation of polycarbonate. Compared to lower rate experiments, we observe higher spall strengths, a higher spall initiation threshold, and a more gradual decrease in spall strength with increasing prior shock stress. This paper provides a strong basis for future computational model development and brings up questions on the underlying mechanisms that control spallation in polymers at extreme strain rates.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-2","pages":"025503"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Physical Review EPub Date : 2025-02-01DOI: 10.1103/PhysRevE.111.025501
Megha Emerse, Lucas Goehring
{"title":"Wrinkling and imaging of thin curved sheets.","authors":"Megha Emerse, Lucas Goehring","doi":"10.1103/PhysRevE.111.025501","DOIUrl":"https://doi.org/10.1103/PhysRevE.111.025501","url":null,"abstract":"<p><p>Thin films or sheets subjected to external forces often undergo mechanical instability, leading to regular patterns of wrinkles, folds, and creases. As can be anticipated from the difficulty of flattening a curved globe, any natural curvature of the sheet will have a strong influence on these instabilities. Here, we develop a noninvasive synthetic schlieren imaging technique to image and reconstruct the surface of wrinkling curved sheets, confined to float on water. Our method circumvents the small-amplitude limit of related imaging techniques, and we demonstrate robust means to estimate the reconstruction accuracy. We then evaluate how the sign and magnitude of Gaussian curvature affect the wrinkling of thin curved sheets, and compare observations of the wrinkle wavelength, amplitude, and domain structure with recent theoretical predictions. While generally validating model predictions, we find that the assumption of a conserved surface area during wrinkling should be treated with some care. The control of wrinkling behavior demonstrated here can have applications in the design of liquid lenses, microfluidics, active textured surfaces, and flexible electronic components.</p>","PeriodicalId":48698,"journal":{"name":"Physical Review E","volume":"111 2-2","pages":"025501"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}