HIGHLIGHTED ARTICLES

Information content of brain states is explained by structural constraints on state energetics

Leon Weninger, Pragya Srivastava, Dale Zhou, Jason Z. Kim, Eli J. Cornblath, Maxwell A. Bertolero, Ute Habel, Dorit Merhof, and Dani S. Bassett

Phys. Rev. E 106, 014401 (2022) - Published 5 July, 2022

The structure of connections in the brain determines how activity can propagate, and hence how brain states can evolve. The authors of this paper find that the human brain structure is especially suited to efficiently reach brain states with a high information content.

Morphological transformation from fibers to sheets in embiopteran silk

Aleimah C. Andrews, Sean Duffy, Janice S. Edgerly, and Richard P. Barber, Jr.

Phys. Rev. E 106, 014801 (2022) - Published 5 July, 2022

Using scanning electron microscopes, researchers have observed how water transforms individual silk threads into protective sheets to create waterproof habitats for web-spinning insects.

Collective effects on the performance and stability of quantum heat engines

Leonardo da Silva Souza, Gonzalo Manzano, Rosario Fazio, and Fernando Iemini

Phys. Rev. E 106, 014143 (2022) - Published 28 July, 2022

The authors of this paper investigate the impact of collective effects on the performance of quantum heat engines, specifically the stability of output power with respect to fluctuations. They show a regime in which one can have enhanced stability for increasing but finite system sizes, while maintaining constant efficiency, which contradicts the classical bound based on the thermodynamic uncertainty relation.

Testing wave turbulence theory for the Gross-Pitaevskii system

Ying Zhu, Boris Semisalov, Giorgio Krstulovic, and Sergey Nazarenko

Phys. Rev. E 106, 014205 (2022) - Published 8 July, 2022

The theory of weak wave turbulence, which describes nonlinear wave interactions, is tested by comparing simulations of the Gross-Pitaevskii equation with the corresponding wave kinetic equation. The authors obtain accurate agreement, with no adjustable parameters, around relevant timescales and provide further validation for using this framework in physically relevant applications.

Forced symmetry breaking as a mechanism for rogue bursts in a dissipative nonlinear dynamical lattice

P. Subramanian, E. Knobloch, and P. G. Kevrekidis

Phys. Rev. E 106, 014212 (2022) - Published 27 July, 2022

A ring of coupled oscillators can form rogue waves, large-amplitude bursts that are localized in space and time. This paper provides an alternative mechanism for the formation of rogue waves in a dissipative nonlinear lattice system, and describes the effect of varying the coupling strength.

Contact map dependence of a T-cell receptor binding repertoire

Kevin Ng Chau, Jason T. George, José N. Onuchic, Xingcheng Lin, and Herbert Levine

Phys. Rev. E 106, 014406 (2022) - Published 27 July, 2022

This paper introduces a contact map to take into account three-dimensional aspects of the interaction between T-cell receptors and peptide histocompatibility complexes. Interactions of these proteins, which are critical to the immune response, had been modeled in previous studies as interactions of linear chains of amino acids. This work demonstrates how incorporating crystal-structure-informed contact maps may affect probabilities for distinguishing foreign from self antigens.

LETTERS

Statistical Physics

Generalization of stochastic-resonance-based threshold networks with Tikhonov regularization

Saiya Bai, Fabing Duan, François Chapeau-Blondeau, and Derek Abbott

Phys. Rev. E 106, L012101 (2022) - Published 6 July, 2022

Nonlinear Dynamics and Chaos

Dancing vortices in a driven nematic liquid crystal cell: Theory and experiment

M. G. Clerc, M. Ferré, R. Gajardo-Pizarro, and V. Zambra

Phys. Rev. E 106, L012201 (2022) - Published 19 July, 2022

Suppression of quasiperiodicity in circle maps with quenched disorder

David Müller-Bender, Johann Luca Kastner, and Günter Radons

Phys. Rev. E 106, L012202 (2022) - Published 22 July, 2022

Networks and Complex Systems

Tropical approximation to finish time of activity networks

Alexei Vazquez

Phys. Rev. E 106, L012301 (2022) - Published 14 July, 2022

Colloids, Complex Fluids, and Active Matter

Interplay between jamming and motility-induced phase separation in persistent self-propelling particles

Jing Yang, Ran Ni, and Massimo Pica Ciamarra

Phys. Rev. E 106, L012601 (2022) - Published 5 July, 2022

Helical flow states in active nematics

Ryan R. Keogh, Santhan Chandragiri, Benjamin Loewe, Tapio Ala-Nissila, Sumesh P. Thampi, and Tyler N. Shendruk

Phys. Rev. E 106, L012602 (2022) - Published 7 July, 2022

Anisotropic active Brownian particle with a fluctuating propulsion force

Jean-Luc Thiffeault and Jiajia Guo

Phys. Rev. E 106, L012603 (2022) - Published 15 July, 2022

Janssen effect in columns of fire ants

Caleb J. Anderson, Pryor A. Gibson, and Alberto Fernandez-Nieves

Phys. Rev. E 106, L012604 (2022) - Published 18 July, 2022

Ratchetlike motion of helical bilayers induced by boundary constraints

Michio Tanaka, Xinyu Wang, Chandan K. Mishra, Jianguo Cai, Jian Feng, Randall D. Kamien, and A. G. Yodh

Phys. Rev. E 106, L012605 (2022) - Published 20 July, 2022

Fluid Dynamics

Conserving elastic turbulence numerically using artificial diffusivity

V. Dzanic, C. S. From, and E. Sauret

Phys. Rev. E 106, L013101 (2022) - Published 12 July, 2022

Plasma Physics

Gyrokinetic electrostatic turbulence close to marginality in the Wendelstein 7-X stellarator

Alessandro Zocco, Linda Podavini, José Manuel Garcìa-Regaña, Michael Barnes, Felix I. Parra, A. Mishchenko, and Per Helander

Phys. Rev. E 106, L013202 (2022) - Published 25 July, 2022

Dust mobilization in the presence of magnetic fields

Li Hsia Yeo, Noah Hood, Xu Wang, and Mihály Horányi

Phys. Rev. E 106, L013203 (2022) - Published 28 July, 2022

ARTICLES

Statistical Physics

Equation of state of hard lenses: A combined virial series and simulation approach

Philipp Marienhagen and Joachim Wagner

Phys. Rev. E 106, 014101 (2022) - Published 1 July, 2022

Statistical properties of large data sets with linear latent features

Philipp Fleig and Ilya Nemenman

Phys. Rev. E 106, 014102 (2022) - Published 5 July, 2022

Statistical physics of inhomogeneous transport: Unification of diffusion laws and inference from first-passage statistics

Roman Belousov, Ali Hassanali, and Édgar Roldán

Phys. Rev. E 106, 014103 (2022) - Published 5 July, 2022

Tensor network renormalization study on the crossover in classical Heisenberg and RP2 models in two dimensions

Atsushi Ueda and Masaki Oshikawa

Phys. Rev. E 106, 014104 (2022) - Published 7 July, 2022

Frustration-induced complexity in order-disorder transitions of the J1J2J3 Ising model on the square lattice

Rodolfo Subert and Bela M. Mulder

Phys. Rev. E 106, 014105 (2022) - Published 7 July, 2022

Universal minimal cost of coherent biochemical oscillations

Lukas Oberreiter, Udo Seifert, and Andre C. Barato

Phys. Rev. E 106, 014106 (2022) - Published 8 July, 2022

Adiabatic lapse rate of real gases

Bogar Díaz, Miguel Ángel García-Ariza, and J. E. Ramírez

Phys. Rev. E 106, 014108 (2022) - Published 11 July, 2022

Projective-truncation-approximation study of the one-dimensional ϕ4 lattice model

Kou-Han Ma, Yan-Jiang Guo, Lei Wang, and Ning-Hua Tong

Phys. Rev. E 106, 014110 (2022) - Published 11 July, 2022

Nonmonotonic heat dissipation phenomenon in close-packed hotspot systems

Chuang Zhang and Lei Wu

Phys. Rev. E 106, 014111 (2022) - Published 11 July, 2022

When stochasticity leads to cooperation

Ian Braga and Lucas Wardil

Phys. Rev. E 106, 014112 (2022) - Published 12 July, 2022

Stationary states in two-lane traffic: Insights from kinetic theory

A. Sai Venkata Ramana and Saif Eddin Jabari

Phys. Rev. E 106, 014113 (2022) - Published 12 July, 2022

Non-Markovian thermal operations boosting the performance of quantum heat engines

Krzysztof Ptaszyński

Phys. Rev. E 106, 014114 (2022) - Published 12 July, 2022

Force density functional theory in- and out-of-equilibrium

Salomée M. Tschopp, Florian Sammüller, Sophie Hermann, Matthias Schmidt, and Joseph M. Brader

Phys. Rev. E 106, 014115 (2022) - Published 12 July, 2022

Learning through atypical phase transitions in overparameterized neural networks

Carlo Baldassi, Clarissa Lauditi, Enrico M. Malatesta, Rosalba Pacelli, Gabriele Perugini, and Riccardo Zecchina

Phys. Rev. E 106, 014116 (2022) - Published 13 July, 2022

Temporal Theil scaling in diffusive trajectory time series

F. S. Abril and C. J. Quimbay

Phys. Rev. E 106, 014117 (2022) - Published 15 July, 2022

Information-driven transitions in projections of underdamped dynamics

Giorgio Nicoletti, Amos Maritan, and Daniel Maria Busiello

Phys. Rev. E 106, 014118 (2022) - Published 18 July, 2022

Preparation of quantum correlations assisted by a steering Maxwell demon

Gang-Gang He and Fu-Lin Zhang

Phys. Rev. E 106, 014119 (2022) - Published 18 July, 2022

Role of extended coupling in bidirectional transport system

Tamizhazhagan S and Atul Kumar Verma

Phys. Rev. E 106, 014120 (2022) - Published 18 July, 2022

Curvature-driven growth and interfacial noise in the voter model with self-induced zealots

Luís Carlos F. Latoski, W. G. Dantas, and Jeferson J. Arenzon

Phys. Rev. E 106, 014121 (2022) - Published 18 July, 2022

Post-thermalization via information spreading in open quantum systems

Krzysztof Ptaszyński and Massimiliano Esposito

Phys. Rev. E 106, 014122 (2022) - Published 18 July, 2022

Polarization-dependent reflection of I-WP minimal-surface-based photonic crystal

Ryosuke Ohnuki, Yuka Kobayashi, and Shinya Yoshioka

Phys. Rev. E 106, 014123 (2022) - Published 19 July, 2022

Reconstructing the dynamical quantum phase transitions via dimensional expansion in a generalized Su-Schrieffer-Heeger model

Xin Li, YuXuan Ma, DuoJia Wang, Yu Wang, and ShunCai Zhao

Phys. Rev. E 106, 014124 (2022) - Published 19 July, 2022

Switching from a continuous to a discontinuous phase transition under quenched disorder

Bartłomiej Nowak and Katarzyna Sznajd-Weron

Phys. Rev. E 106, 014125 (2022) - Published 19 July, 2022

Critical dynamics of the superfluid phase transition: Multiloop calculation of the microscopic model

J. Honkonen, M. Komarova, Yu. Molotkov, M. Nalimov, and A. Trenogin

Phys. Rev. E 106, 014126 (2022) - Published 19 July, 2022

Memory in quantum dot blinking

Roberto N. Muñoz, Laszlo Frazer, Gangcheng Yuan, Paul Mulvaney, Felix A. Pollock, and Kavan Modi

Phys. Rev. E 106, 014127 (2022) - Published 21 July, 2022

Slow dynamics and large deviations in classical stochastic Fredkin chains

Luke Causer, Juan P. Garrahan, and Austen Lamacraft

Phys. Rev. E 106, 014128 (2022) - Published 21 July, 2022

Hysteresis and return point memory in the random-field Blume-Capel model

B. E. Aldrin, Abdul Khaleque, and Sumedha

Phys. Rev. E 106, 014129 (2022) - Published 22 July, 2022

Brownian motion theory of the two-dimensional quantum vortex gas

Hiroshi Kuratsuji

Phys. Rev. E 106, 014130 (2022) - Published 22 July, 2022

Counterdiabatic driving in the classical β-Fermi-Pasta-Ulam-Tsingou chain

Nik O. Gjonbalaj, David K. Campbell, and Anatoli Polkovnikov

Phys. Rev. E 106, 014131 (2022) - Published 22 July, 2022

Statistical properties of the off-diagonal matrix elements of observables in eigenstates of integrable systems

Yicheng Zhang, Lev Vidmar, and Marcos Rigol

Phys. Rev. E 106, 014132 (2022) - Published 25 July, 2022

Microseismic event detection in noisy environments with instantaneous spectral Shannon entropy

Sérgio Luiz E. F. da Silva and Gilberto Corso

Phys. Rev. E 106, 014133 (2022) - Published 25 July, 2022

Evidence for additional third-order transitions in the two-dimensional Ising model

Kedkanok Sitarachu and Michael Bachmann

Phys. Rev. E 106, 014134 (2022) - Published 25 July, 2022

Dynamic crossover towards energy equipartition in the Fermi-Pasta-Ulam-Tsingou β model with long-range interactions

Jian Wang and Ai-chen Li

Phys. Rev. E 106, 014135 (2022) - Published 25 July, 2022

Fock-space approach to stochastic susceptible-infected-recovered models

Danillo B. de Souza, Hugo A. Araújo, Gerson C. Duarte-Filho, Eamonn A. Gaffney, Fernando A. N. Santos, and Ernesto P. Raposo

Phys. Rev. E 106, 014136 (2022) - Published 25 July, 2022

Spectral fingerprints of nonequilibrium dynamics: The case of a Brownian gyrator

Sara Cerasoli, Sergio Ciliberto, Enzo Marinari, Gleb Oshanin, Luca Peliti, and Lamberto Rondoni

Phys. Rev. E 106, 014137 (2022) - Published 26 July, 2022

Optimal charging of open spin-chain quantum batteries via homodyne-based feedback control

Y. Yao and X. Q. Shao

Phys. Rev. E 106, 014138 (2022) - Published 27 July, 2022

Diffusion on a lattice: Transition rates, interactions, and memory effects

M. A. Di Muro and M. Hoyuelos

Phys. Rev. E 106, 014139 (2022) - Published 27 July, 2022

Estimation of drift and diffusion functions from unevenly sampled time-series data

William Davis and Bruce Buffett

Phys. Rev. E 106, 014140 (2022) - Published 27 July, 2022

Derivation of a statistical model for classical systems obeying the fractional exclusion principle

Projesh Kumar Roy

Phys. Rev. E 106, 014141 (2022) - Published 28 July, 2022

Random-walk shielding-potential viscosity model for warm dense metals

Yuqing Cheng, Haifeng Liu, Yong Hou, Xujun Meng, Qiong Li, Yu Liu, Xingyu Gao, Jianmin Yuan, Haifeng Song, and Jianguo Wang

Phys. Rev. E 106, 014142 (2022) - Published 28 July, 2022

Collective effects on the performance and stability of quantum heat engines

Leonardo da Silva Souza, Gonzalo Manzano, Rosario Fazio, and Fernando Iemini

Phys. Rev. E 106, 014143 (2022) - Published 28 July, 2022

The authors of this paper investigate the impact of collective effects on the performance of quantum heat engines, specifically the stability of output power with respect to fluctuations. They show a regime in which one can have enhanced stability for increasing but finite system sizes, while maintaining constant efficiency, which contradicts the classical bound based on the thermodynamic uncertainty relation.

Molecular hints of two-step transition to convective flow via streamline percolation

P. L. Garrido and P. I. Hurtado

Phys. Rev. E 106, 014144 (2022) - Published 28 July, 2022

Perturbative expansion of irreversible work in symmetric and asymmetric processes

T. Koide

Phys. Rev. E 106, 014145 (2022) - Published 28 July, 2022

Spacing distribution in the two-dimensional Coulomb gas: Surmise and symmetry classes of non-Hermitian random matrices at noninteger β

Gernot Akemann, Adam Mielke, and Patricia Päßler

Phys. Rev. E 106, 014146 (2022) - Published 28 July, 2022

Stochastic representation of processes with resetting

Marcin Magdziarz and Kacper Taźbierski

Phys. Rev. E 106, 014147 (2022) - Published 28 July, 2022

Finite-size scaling of critical avalanches

Avinash Chand Yadav, Abdul Quadir, and Haider Hasan Jafri

Phys. Rev. E 106, 014148 (2022) - Published 28 July, 2022

Frustration in a generalized kagomé Ising antiferromagnet: Exact results

K. A. Muttalib and J. H. Barry

Phys. Rev. E 106, 014149 (2022) - Published 29 July, 2022

Steady states and coarsening in one-dimensional driven Allen-Cahn system

Rajiv G. Pereira

Phys. Rev. E 106, 014150 (2022) - Published 29 July, 2022

Lower critical dimension of the random-field XY model and the zero-temperature critical line

Kutay Akın and A. Nihat Berker

Phys. Rev. E 106, 014151 (2022) - Published 29 July, 2022

Numerically probing the universal operator growth hypothesis

Robin Heveling, Jiaozi Wang, and Jochen Gemmer

Phys. Rev. E 106, 014152 (2022) - Published 29 July, 2022

Mutual information in changing environments: Nonlinear interactions, out-of-equilibrium systems, and continuously varying diffusivities

Giorgio Nicoletti and Daniel Maria Busiello

Phys. Rev. E 106, 014153 (2022) - Published 29 July, 2022

Full counting statistics and fluctuation theorem for the currents in the discrete model of Feynman's ratchet

Yu-Xin Wu, Jiayin Gu, and H. T. Quan

Phys. Rev. E 106, 014154 (2022) - Published 29 July, 2022

Nonlinear Dynamics and Chaos

Stability limits for modes held in alternating trapping-expulsive potentials

Zhihuan Luo, Yan Liu, Yongyao Li, Josep Batle, and Boris A. Malomed

Phys. Rev. E 106, 014201 (2022) - Published 1 July, 2022

Regulating dynamics through intermittent interactions

Shiva Dixit, Manaoj Aravind, and P. Parmananda

Phys. Rev. E 106, 014203 (2022) - Published 7 July, 2022

Estimating asymptotic phase and amplitude functions of limit-cycle oscillators from time series data

Norihisa Namura, Shohei Takata, Katsunori Yamaguchi, Ryota Kobayashi, and Hiroya Nakao

Phys. Rev. E 106, 014204 (2022) - Published 7 July, 2022

Testing wave turbulence theory for the Gross-Pitaevskii system

Ying Zhu, Boris Semisalov, Giorgio Krstulovic, and Sergey Nazarenko

Phys. Rev. E 106, 014205 (2022) - Published 8 July, 2022

The theory of weak wave turbulence, which describes nonlinear wave interactions, is tested by comparing simulations of the Gross-Pitaevskii equation with the corresponding wave kinetic equation. The authors obtain accurate agreement, with no adjustable parameters, around relevant timescales and provide further validation for using this framework in physically relevant applications.

Sublinear diffusion in the generalized triangle map

Kensuke Yoshida, Giulio Casati, Shingo Watanabe, and Akira Shudo

Phys. Rev. E 106, 014206 (2022) - Published 11 July, 2022

Dynamical buckling of a table-tennis ball impinging normally on a rigid target: Experimental and numerical studies

Théophile Rémond, Vincent Dolique, Franck Vittoz, Sheedev Antony, Renaud G. Rinaldi, Lionel Manin, and Jean-Christophe Géminard

Phys. Rev. E 106, 014207 (2022) - Published 12 July, 2022

Super rogue waves: Collision of rogue waves in Bose-Einstein condensate

Yanchang Tan, Xiao-Dong Bai, and Tiantian Li

Phys. Rev. E 106, 014208 (2022) - Published 12 July, 2022

Bistability and chaos-assisted tunneling in dissipative quantum systems

Andrey R. Kolovsky

Phys. Rev. E 106, 014209 (2022) - Published 14 July, 2022

Boundary chaos

Felix Fritzsch and Tomaž Prosen

Phys. Rev. E 106, 014210 (2022) - Published 15 July, 2022

Fluctuation properties of the eigenfrequencies and scattering matrix of closed and open unidirectional graphs with chaotic wave dynamics

Jiongning Che, Xiaodong Zhang, Weihua Zhang, Barbara Dietz, and Guozhi Chai

Phys. Rev. E 106, 014211 (2022) - Published 25 July, 2022

Forced symmetry breaking as a mechanism for rogue bursts in a dissipative nonlinear dynamical lattice

P. Subramanian, E. Knobloch, and P. G. Kevrekidis

Phys. Rev. E 106, 014212 (2022) - Published 27 July, 2022

A ring of coupled oscillators can form rogue waves, large-amplitude bursts that are localized in space and time. This paper provides an alternative mechanism for the formation of rogue waves in a dissipative nonlinear lattice system, and describes the effect of varying the coupling strength.

Chaos and thermalization in a classical chain of dipoles

Manuel Iñarrea, Rosario González-Férez, J. Pablo Salas, and Peter Schmelcher

Phys. Rev. E 106, 014213 (2022) - Published 27 July, 2022

Modulation instability of an electromagnetic wave interacting with a counterpropagating electron beam under condition of cyclotron resonance absorption

A. A. Rostuntsova, N. M. Ryskin, I. V. Zotova, and N. S. Ginzburg

Phys. Rev. E 106, 014214 (2022) - Published 28 July, 2022

Networks and Complex Systems

Adversarial attacks on voter model dynamics in complex networks

Katsumi Chiyomaru and Kazuhiro Takemoto

Phys. Rev. E 106, 014301 (2022) - Published 5 July, 2022

Reconstructing distant interactions of multiple paths between perceptible nodes in dark networks

Xinyu Wang, Yuanyuan Mi, Zhaoyang Zhang, Yang Chen, Gang Hu, and Haihong Li

Phys. Rev. E 106, 014302 (2022) - Published 5 July, 2022

Absorbing phase transition in a unidirectionally coupled layered network

Manoj C. Warambhe, Ankosh D. Deshmukh, and Prashant M. Gade

Phys. Rev. E 106, 014303 (2022) - Published 8 July, 2022

N-strain epidemic model using bond percolation

Peter Mann, V. Anne Smith, John B. O. Mitchell, and Simon Dobson

Phys. Rev. E 106, 014304 (2022) - Published 20 July, 2022

Solving a directed-percolation inverse problem

Sean Deyo

Phys. Rev. E 106, 014305 (2022) - Published 21 July, 2022

Inferring spatial source of disease outbreaks using maximum entropy

Mehrad Ansari, David Soriano-Paños, Gourab Ghoshal, and Andrew D. White

Phys. Rev. E 106, 014306 (2022) - Published 21 July, 2022

Effect of initial infection size on a network susceptible-infected-recovered model

G. Machado and G. J. Baxter

Phys. Rev. E 106, 014307 (2022) - Published 21 July, 2022

Moment closure approximations of susceptible-infected-susceptible epidemics on adaptive networks

Massimo A. Achterberg and Piet Van Mieghem

Phys. Rev. E 106, 014308 (2022) - Published 25 July, 2022

Effects of time-varying habitat connectivity on metacommunity persistence

Subhendu Bhandary, Debabrata Biswas, Tanmoy Banerjee, and Partha Sharathi Dutta

Phys. Rev. E 106, 014309 (2022) - Published 25 July, 2022

Biological Physics

Information content of brain states is explained by structural constraints on state energetics

Leon Weninger, Pragya Srivastava, Dale Zhou, Jason Z. Kim, Eli J. Cornblath, Maxwell A. Bertolero, Ute Habel, Dorit Merhof, and Dani S. Bassett

Phys. Rev. E 106, 014401 (2022) - Published 5 July, 2022

The structure of connections in the brain determines how activity can propagate, and hence how brain states can evolve. The authors of this paper find that the human brain structure is especially suited to efficiently reach brain states with a high information content.

Self-sustaining oscillation of two axonemal microtubules based on a stochastic bonding model between microtubules and dynein

T. Omori, S. Munakata, and T. Ishikawa

Phys. Rev. E 106, 014402 (2022) - Published 7 July, 2022

Gene-influx-driven evolution

David B. Saakian and Eugene V. Koonin

Phys. Rev. E 106, 014403 (2022) - Published 12 July, 2022

Free-energy landscapes and insertion pathways for peptides in membrane environment

Ganga P. Sharma, Aaron C. Meyer, Suhail Habeeb, Michael Karbach, and Gerhard Müller

Phys. Rev. E 106, 014404 (2022) - Published 20 July, 2022

Intrinsic equilibrium of stably autorotating samaras

Peixing Niu, Michael D. Atkins, Yanyan Liu, Moxiao Li, Tian Jian Lu, and Tongbeum Kim

Phys. Rev. E 106, 014405 (2022) - Published 26 July, 2022

Contact map dependence of a T-cell receptor binding repertoire

Kevin Ng Chau, Jason T. George, José N. Onuchic, Xingcheng Lin, and Herbert Levine

Phys. Rev. E 106, 014406 (2022) - Published 27 July, 2022

This paper introduces a contact map to take into account three-dimensional aspects of the interaction between T-cell receptors and peptide histocompatibility complexes. Interactions of these proteins, which are critical to the immune response, had been modeled in previous studies as interactions of linear chains of amino acids. This work demonstrates how incorporating crystal-structure-informed contact maps may affect probabilities for distinguishing foreign from self antigens.

Estimating near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules

Maciej Długosz, Bogdan Cichocki, and Piotr Szymczak

Phys. Rev. E 106, 014407 (2022) - Published 29 July, 2022

Polymers

Computational indentation in highly cross-linked polymer networks

Manoj Kumar Maurya, Céline Ruscher, Debashish Mukherji, and Manjesh Kumar Singh

Phys. Rev. E 106, 014501 (2022) - Published 6 July, 2022

Decoding polymer self-dynamics using a two-step approach

Zhiqiang Shen, Jan-Michael Y. Carrillo, Bobby G. Sumpter, and Yangyang Wang

Phys. Rev. E 106, 014502 (2022) - Published 11 July, 2022

Deep learning and inverse discovery of polymer self-consistent field theory inspired by physics-informed neural networks

Danny Lin and Hsiu-Yu Yu

Phys. Rev. E 106, 014503 (2022) - Published 25 July, 2022

Migration of active rings in porous media

Ligesh Theeyancheri, Subhasish Chaki, Tapomoy Bhattacharjee, and Rajarshi Chakrabarti

Phys. Rev. E 106, 014504 (2022) - Published 28 July, 2022

Tensile strength of rubber described via the formation and rupture of load-bearing polymer chains

Reinhard Hentschke

Phys. Rev. E 106, 014505 (2022) - Published 29 July, 2022

Molecular signatures of the glass transition in polymers

Tianyi Jin (金天逸), Connor W. Coley, and Alfredo Alexander-Katz

Phys. Rev. E 106, 014506 (2022) - Published 29 July, 2022

Colloids, Complex Fluids, and Active Matter

Stokes traction on an active particle

Günther Turk, Rajesh Singh, and Ronojoy Adhikari

Phys. Rev. E 106, 014601 (2022) - Published 5 July, 2022

Enhancement in the diffusivity of Brownian spheroids in the presence of spheres

Vikki Anand Varma, Isha Malhotra, and Sujin B. Babu

Phys. Rev. E 106, 014602 (2022) - Published 14 July, 2022

Group formation and collective motion of colloidal rods with an activity triggered by visual perception

Philipp Stengele, Anton Lüders, and Peter Nielaba

Phys. Rev. E 106, 014603 (2022) - Published 14 July, 2022

Structural relaxation dynamics of colloidal nanotrimers

Justinas Šlepavičius, Carlos Avendaño, Breanndán Ó. Conchúir, and Alessandro Patti

Phys. Rev. E 106, 014604 (2022) - Published 15 July, 2022

Inertial active Ornstein-Uhlenbeck particle in the presence of a magnetic field

M. Muhsin and M. Sahoo

Phys. Rev. E 106, 014605 (2022) - Published 20 July, 2022

Collective dynamics of liquid sulfur scrutinized over three decades in frequency

F. Demmel and M. Jimenez-Ruiz

Phys. Rev. E 106, 014606 (2022) - Published 21 July, 2022

Anisotropic correlations of plasticity on the yielding of metallic glasses

Shiheng Cui, Huashan Liu, and Hailong Peng

Phys. Rev. E 106, 014607 (2022) - Published 21 July, 2022

Explicit solvent effects on macromolecular interactions from a solvent-augmented contact value theorem

Sahin Buyukdagli

Phys. Rev. E 106, 014608 (2022) - Published 21 July, 2022

Information conduction and convection in noiseless Vicsek flocks

Daniel Geiß, Klaus Kroy, and Viktor Holubec

Phys. Rev. E 106, 014609 (2022) - Published 21 July, 2022

Short-range and long-range correlations in driven dense colloidal mixtures in narrow pores

František Slanina, Miroslav Kotrla, and Karel Netočný

Phys. Rev. E 106, 014610 (2022) - Published 25 July, 2022

Transition in collective motion decision making

Biao Wang, Yue Wu, Guangwei Wang, Lan Liu, Guanrong Chen, and Hai-Tao Zhang

Phys. Rev. E 106, 014611 (2022) - Published 25 July, 2022

Internal-stress-induced solid-solid transition involving orientational domains of anisotropic particles

Tao Huang, Chunhua Zeng, Hua Wang, Yong Chen, and Yilong Han

Phys. Rev. E 106, 014612 (2022) - Published 26 July, 2022

Active responsive colloids coupled to different thermostats

Polina Gaindrik, Upayan Baul, and Joachim Dzubiella

Phys. Rev. E 106, 014613 (2022) - Published 26 July, 2022

Structural properties of liquids in extreme confinement

Gerhard Jung and Thomas Franosch

Phys. Rev. E 106, 014614 (2022) - Published 27 July, 2022

Bistability in orbital trajectories of a chiral self-propelled particle interacting with an external field

G. A. Patterson

Phys. Rev. E 106, 014615 (2022) - Published 28 July, 2022

Shear viscosity and Stokes-Einstein violation in supercooled light and heavy water

Pierre Ragueneau, Frédéric Caupin, and Bruno Issenmann

Phys. Rev. E 106, 014616 (2022) - Published 28 July, 2022

Active colloidal molecules in activity gradients

Hidde D. Vuijk, Sophie Klempahn, Holger Merlitz, Jens-Uwe Sommer, and Abhinav Sharma

Phys. Rev. E 106, 014617 (2022) - Published 29 July, 2022

Liquid Crystals

Determining the Kerr constant in optically isotropic liquid crystals

Tetiana Yevchenko, Dorota Dardas, Wojciech Kuczyński, and Arkadiusz C. Brańka

Phys. Rev. E 106, 014701 (2022) - Published 1 July, 2022

Nonequilibrium phase transitions of a nematic liquid crystal under ac field-driven electroconvection

Jong-Hoon Huh

Phys. Rev. E 106, 014702 (2022) - Published 1 July, 2022

Peculiarities of focal conic structure formed near the cholesteric-isotropic phase transition

P. V. Dolganov, K. D. Baklanova, and V. K. Dolganov

Phys. Rev. E 106, 014703 (2022) - Published 13 July, 2022

Structure and optical properties of twist-bend nematic liquid crystals doped with chiral dopants

Xinfang Zhang, Ziyuan Zhou, Yunho Shin, Suman Halder, Lang Hu, and Deng-Ke Yang

Phys. Rev. E 106, 014704 (2022) - Published 13 July, 2022

Nematic order condensation and topological defects in inertial active nematics

Roozbeh Saghatchi, Mehmet Yildiz, and Amin Doostmohammadi

Phys. Rev. E 106, 014705 (2022) - Published 25 July, 2022

Anisotropic viscous effects of local flow by a rotating microparticle in nematic liquid crystal

Jun-Yong Lee, Jae Hoon Lee, Bohdan Lev, and Jong-Hyun Kim

Phys. Rev. E 106, 014706 (2022) - Published 25 July, 2022

Films and Interfaces

Morphological transformation from fibers to sheets in embiopteran silk

Aleimah C. Andrews, Sean Duffy, Janice S. Edgerly, and Richard P. Barber, Jr.

Phys. Rev. E 106, 014801 (2022) - Published 5 July, 2022

Using scanning electron microscopes, researchers have observed how water transforms individual silk threads into protective sheets to create waterproof habitats for web-spinning insects.

Interface collisions with diffusive mass transport

Bastien Marguet, F. D. A. Aarão Reis, and Olivier Pierre-Louis

Phys. Rev. E 106, 014802 (2022) - Published 14 July, 2022

Perturbing the catenoid: Stability and mechanical properties of nonaxisymmetric minimal surfaces

Friedrich Walzel, Alice Requier, Kevin Boschi, Jean Farago, Philippe Fuchs, Fabrice Thalmann, Wiebke Drenckhan, Pierre Muller, and Thierry Charitat

Phys. Rev. E 106, 014803 (2022) - Published 22 July, 2022

Granular Materials

Drag on a circular intruder traversing a shape-heterogeneous granular mixture

Bitang Kwrung Tripura, Sonu Kumar, Vamsi Krishna Reddy Anyam, and K. Anki Reddy

Phys. Rev. E 106, 014901 (2022) - Published 7 July, 2022

Unified penetration depth of low-velocity intruders into granular packings

Thanh-Trung Vo and Trung-Kien Nguyen

Phys. Rev. E 106, 014902 (2022) - Published 20 July, 2022

Volume-shear coupling in a mesoscopic model of amorphous materials

E. A. Jagla

Phys. Rev. E 106, 014903 (2022) - Published 22 July, 2022

Continuous to intermittent flows in growing granular heaps

L. Alonso-Llanes, E. Martínez, A. J Batista-Leyva, R. Toussaint, and E. Altshuler

Phys. Rev. E 106, 014904 (2022) - Published 25 July, 2022

Decompaction wave propagation in a vibrated fine-powder bed

Prasad Sonar and Hiroaki Katsuragi

Phys. Rev. E 106, 014905 (2022) - Published 27 July, 2022

Successive reintrusions in a granular medium

B. Darbois Texier and A. Seguin

Phys. Rev. E 106, 014906 (2022) - Published 28 July, 2022

Solid Mechanics

Anomalous elasticity in classical glass formers

Avanish Kumar, Michael Moshe, Itamar Procaccia, and Murari Singh

Phys. Rev. E 106, 015001 (2022) - Published 7 July, 2022

Stress-free morphing by means of compatible distortions

Ivan Colorado-Cervantes, Valerio Varano, and Luciano Teresi

Phys. Rev. E 106, 015003 (2022) - Published 12 July, 2022

Effect of architecture disorder on the elastic response of two-dimensional lattice materials

Antoine Montiel, Thuy Nguyen, Cindy L. Rountree, Valérie Geertsen, Patrick Guenoun, and Daniel Bonamy

Phys. Rev. E 106, 015004 (2022) - Published 19 July, 2022

Geometric thermodynamics of strain-induced crystallization in polymers

Sanhita Das, Asif Raza, and Debasish Roy

Phys. Rev. E 106, 015005 (2022) - Published 25 July, 2022

Fluid Dynamics

Extreme events and instantons in Lagrangian passive scalar turbulence models

Mnerh Alqahtani, Leonardo Grigorio, and Tobias Grafke

Phys. Rev. E 106, 015101 (2022) - Published 1 July, 2022

Discrete Boltzmann modeling of Rayleigh-Taylor instability: Effects of interfacial tension, viscosity, and heat conductivity

Jie Chen, Aiguo Xu, Dawei Chen, Yudong Zhang, and Zhihua Chen

Phys. Rev. E 106, 015102 (2022) - Published 11 July, 2022

Nanoparticle transport within non-Newtonian fluid flow in porous media

Takshak Shende, Deepak Mangal, Jacinta C. Conrad, Vahid Niasar, and Masoud Babaei

Phys. Rev. E 106, 015103 (2022) - Published 11 July, 2022

Numerical simulation of superparamagnetic nanoparticle motion in blood vessels for magnetic drug delivery

Matthew Lee, Aditya Shelke, Saloni Singh, Jenny Fan, Philip Zaleski, and Shahriar Afkhami

Phys. Rev. E 106, 015104 (2022) - Published 12 July, 2022

Influence of particle shape and material on the acoustic radiation force and microstreaming in a standing wave

Alen Pavlic, Pushkin Nagpure, Lorenzo Ermanni, and Jürg Dual

Phys. Rev. E 106, 015105 (2022) - Published 13 July, 2022

Numerical study on the Leidenfrost behavior of a droplet stream impinging on a heated wall

Kshitiz Kumar Subedi and Song-Charng Kong

Phys. Rev. E 106, 015106 (2022) - Published 15 July, 2022

Residence time distributions for in-line chaotic mixers

Nelson Poumaëre, Benoît Pier, and Florence Raynal

Phys. Rev. E 106, 015107 (2022) - Published 19 July, 2022

Diffusion tensor imaging of anisotropic inhomogeneous turbulent flow

Amy-Rae P. Gauthier, Noah Stocek, and Benedict Newling

Phys. Rev. E 106, 015108 (2022) - Published 22 July, 2022

Cylindrical convergence effects on the Rayleigh-Taylor instability in elastic and viscous media

A. R. Piriz, S. A. Piriz, and N. A. Tahir

Phys. Rev. E 106, 015109 (2022) - Published 22 July, 2022

Phase-field numerical study on the dynamic process of thermocapillary patterning

Qingzhen Yang, Yankui Liu, Xinmiao Jia, Tingting Zhang, Hongmiao Tian, Jing Fan, Quange Xu, and Fenhong Song

Phys. Rev. E 106, 015111 (2022) - Published 29 July, 2022

Plasma Physics

Vacuum breakdown in magnetic dipole wave by 10-PW class lasers

E. S. Efimenko, A. V. Bashinov, A. A. Muraviev, V. D. Volokitin, I. B. Meyerov, G. Leuchs, A. M. Sergeev, and A. V. Kim

Phys. Rev. E 106, 015201 (2022) - Published 11 July, 2022

Directional locking in a two-dimensional Yukawa solid modulated by a two-dimensional periodic substrate

Wenqi Zhu, C. Reichhardt, C. J. O. Reichhardt, and Yan Feng

Phys. Rev. E 106, 015202 (2022) - Published 15 July, 2022

Fast particles overtaking shock front in two-dimensional Yukawa solids

Pengwei Qiu and Yan Feng

Phys. Rev. E 106, 015203 (2022) - Published 21 July, 2022

One-component plasma of a million particles via angular-averaged Ewald potential: A Monte Carlo study

G. S. Demyanov and P. R. Levashov

Phys. Rev. E 106, 015204 (2022) - Published 26 July, 2022

Ionization states for the multipetawatt laser-QED regime

I. Ouatu, B. T. Spiers, R. Aboushelbaya, Q. Feng, M. W. von der Leyen, R. W. Paddock, R. Timmis, C. Ticos, K. M. Krushelnick, and P. A. Norreys

Phys. Rev. E 106, 015205 (2022) - Published 27 July, 2022

Plasma environmental effects in the atomic structure for simulating x-ray free-electron-laser-heated solid-density matter

Rui Jin, Zoltan Jurek, Robin Santra, and Sang-Kil Son

Phys. Rev. E 106, 015206 (2022) - Published 29 July, 2022

Computational Physics

Particles on demand for flows with strong discontinuities

N. G. Kallikounis, B. Dorschner, and I. V. Karlin

Phys. Rev. E 106, 015301 (2022) - Published 5 July, 2022

Resolution exchange with tunneling for enhanced sampling of protein landscapes

Fatih Yasar, Alan J. Ray, and Ulrich H. E. Hansmann

Phys. Rev. E 106, 015302 (2022) - Published 5 July, 2022

Asymptotic method for entropic multiple relaxation time model in lattice Boltzmann method

Xiangshuo Tang, Yue Yu, and Alparslan Oztekin

Phys. Rev. E 106, 015303 (2022) - Published 7 July, 2022

Multiscale analysis of the particles on demand kinetic model

Ehsan Reyhanian

Phys. Rev. E 106, 015304 (2022) - Published 8 July, 2022

Modeling fluid polyamorphism through a maximum-valence approach

Nikolay A. Shumovskyi, Thomas J. Longo, Sergey V. Buldyrev, and Mikhail A. Anisimov

Phys. Rev. E 106, 015305 (2022) - Published 11 July, 2022

Diffuse-interface lattice Boltzmann modeling of charged particle transport in Poiseuille flow

Jiao Liu, Zhenhua Chai, and Baochang Shi

Phys. Rev. E 106, 015306 (2022) - Published 18 July, 2022

Multiphase curved boundary condition in lattice Boltzmann method

Yichen Yao, Yangsha Liu, Xingguo Zhong, and Binghai Wen

Phys. Rev. E 106, 015307 (2022) - Published 20 July, 2022

Accuracy and performance of the lattice Boltzmann method with 64-bit, 32-bit, and customized 16-bit number formats

Moritz Lehmann, Mathias J. Krause, Giorgio Amati, Marcello Sega, Jens Harting, and Stephan Gekle

Phys. Rev. E 106, 015308 (2022) - Published 26 July, 2022

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