Article
Evolutionary Biology
Vadim Goremykin
Summary: Evaluating the absolute fit of substitution models to phylogenetic data is important for reliable phylogenetic inference. The loss of information in previous methods negatively affects discriminatory power and sensitivity to lineage-specific changes. A novel statistic is proposed as an alternative method, which exhibits greater discriminatory power and can accommodate gaps and lineage-specific shifts. The method can be implemented in both Bayesian and Maximum Likelihood analyses, emphasizing the importance of model fit assessment.
SYSTEMATIC BIOLOGY
(2023)
Article
Computer Science, Interdisciplinary Applications
Ondrej Kincl, Michal Pavelka
Summary: This paper presents an energy-preserving and globally time-reversible code for weakly compressible smoothed particle hydrodynamics (SPH). The equations are discretized using a corrected expression for density and a symplectic integrator, without adding additional dynamics at the level of ordinary differential equation. To achieve global-in-time reversibility, the authors correct the initial state, implement a conservative fluid-wall interaction, and use fixed-point arithmetic. Despite being globally reversible, the numerical scheme exhibits thermalization of particle velocities and growth of Boltzmann entropy, indicating the emergence of irreversible behavior from reversible dynamics.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Mathematics, Applied
Wei Liu
Summary: This study investigates the moment stability of a class of time-changed stochastic differential equations with coefficients allowed to grow super-linearly. It is shown that the decay rate is polynomial for certain types of subordinators, which differs significantly from classical SDEs driven by Brownian motion.
APPLIED MATHEMATICS LETTERS
(2021)
Article
Chemistry, Physical
Ying Zhang, Pan Luo, Ya Liu, Hanmin Li, Xiaojiang Li, Hongsheng Lu, Yuanpeng Wu, Dongfang Liu
Summary: Solid-stabilized high internal phase emulsions have received significant attention in recent years. A new type of high internal phase non-Pickering emulsion, stabilized by electrostatic repulsion between surfactants and hydrophilic solid particles, has been successfully prepared. Unlike traditional high internal phase Pickering emulsions, the solid particles are dispersed in the continuous phase rather than existing at the oil-water interface. Moreover, the emulsion exhibits similar rheological behavior, allowing for the conversion between different types of high internal phase emulsions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Automation & Control Systems
Yury Orlov
Summary: A novel approach is proposed for the prescribed-time stabilizing design of feedback linearizable controllable systems. The approach involves scaling the finite-time stabilizing non-Lipschitz feedback by means of time deformation and changing the state variables. The resulting feedback design has time-varying gains that are uniformly bounded, offering an attractive implementation opportunity compared to existing methods.
Article
Multidisciplinary Sciences
Dusan Kolarski, Carla Miro-Vinyals, Akiko Sugiyama, Ashutosh Srivastava, Daisuke Ono, Yoshiko Nagai, Mui Iida, Kenichiro Itami, Florence Tama, Wiktor Szymanski, Tsuyoshi Hirota, Ben L. Feringa
Summary: This study presents the development of a visible light-responsive inhibitor of casein kinase I, enabling precise and reversible control of cellular and tissue circadian rhythms. The inhibitor can switch between CKI isoforms and reveal the importance of CKI delta in period regulation, allowing for long-term regulation of CKI activity and reversible modulation of circadian rhythms through chronophotopharmacology.
NATURE COMMUNICATIONS
(2021)
Article
Mathematics, Applied
Paulo L. Dattori L. da Silva, To Fu Ma, Edwin M. M. Maravi-Percca, Paulo N. N. Seminario-Huertas
Summary: This paper focuses on the asymptotic stability of the Lame system, which is widely used in seismology and isotropic elasticity. The key feature lies in the well-posedness and energy decay when there is a time-dependent delay and frictional damping. By treating the problem as a Cauchy problem with time-dependent operators, we employ Kato's CD-system method. A simple argument is presented to prove the required stability for a family of time-dependent semigroup generators.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2023)
Article
Multidisciplinary Sciences
Gong Chen, Colin Ophus, Alberto Quintana, Heeyoung Kwon, Changyeon Won, Haifeng Ding, Yizheng Wu, Andreas K. Schmid, Kai Liu
Summary: In this study, a novel approach of using hydrogen adsorption for writing and deleting skyrmions at room temperature was demonstrated. Through Monte-Carlo simulations, it was found that hydrogen-induced magnetic anisotropy change led to the creation and annihilation of skyrmions. Additionally, the effects of hydrogen and oxygen on magnetic anisotropy and skyrmion deletion on other magnetic surfaces were also explored.
NATURE COMMUNICATIONS
(2022)
Article
Nanoscience & Nanotechnology
Xuan Liu, Hanbing Wang, Junsen Zhong, Menghan Li, Rui Zhang, Dongjiang You, Lingyu Du, Yanfeng Gao, Litao Kang
Summary: In this paper, a novel electrochromic system based on reversible oxide electro-deposition/dissolution is developed for EC windows. The system exhibits high optical modulation amplitude and shows no deterioration within 1000 switching cycles. This work is significant for the exploration of novel ROE-type EC systems.
Article
Mathematics, Interdisciplinary Applications
Xing Zhu, Shangwen Liao, Zhen Cai, Yunli Qiu, Yingji He
Summary: The study demonstrates the existence and stability of continuous soliton families in Kerr media with two-dimensional non-parity-time symmetric complex potentials. Discrete eigenvalues in the linear spectra of these complex potentials are observed, with fundamental solitons bifurcating from the largest discrete eigenvalue and dipole solitons from the second or third largest. Eigenvalues in the soliton linear-stability spectra are found to emerge as complex conjugate pairs, with the impact of different parameters on soliton stability discussed in detail. Additionally, transverse energy flow vectors of the solitons in these complex potentials are investigated.
CHAOS SOLITONS & FRACTALS
(2021)
Article
Engineering, Multidisciplinary
Fanchao Kong, Honglin Ni, Quanxin Zhu, Cheng Hu, Tingwen Huang
Summary: This paper investigates the fixed-time and predefined-time synchronization of discontinuous neutral-type competitive networks with time-scales. By establishing new stability lemmas and control strategies, the authors propose new criteria for the synchronization and improve the effectiveness of previous methods.
IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING
(2023)
Article
Chemistry, Physical
Renpeng Chen, Qin Liu, Lin Xu, Xuri Zuo, Fang Liu, Jianyong Zhang, Xuan Zhou, Liqiang Mai
Summary: A bifunctional poly zwitterionic ionic liquid (PZIL) is designed as a new ion-migration layer to suppress Zn dendrites and side reactions. By guiding the distribution of Zn ions and forming a water-poor interface, it enables stable and reversible performance of Zn-ion batteries.
ACS ENERGY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Zizhen Zeng, Jibao Zhu, Xiaoyu Deng, Huanwen Chen, Yi Jin, Emeric Miclet, Valerie Alezra, Yang Wan
Summary: A new concept for reversible peptide stapling has been developed, which involves macrocyclization and decyclization using dual 1,4-elimination. This strategy enables selective peptide delivery to intracellular or extracellular targets. The study also demonstrates the application of reversibly stapled peptides and the activation of their biological activity through dual 1,4-elimination. These findings contribute to significant advancements in the field of peptide delivery.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Rahi M. Reja, Wenjian Wang, Yuhan Lyu, Fredrik Haeffner, Jianmin Gao
Summary: We report a new reversible lysine conjugation method that shows a unique diazaborine product and slower dissociation kinetics compared to the known iminoboronate chemistry. By incorporating the diazaborine-forming warhead RMR1 into a peptide ligand, we have developed potent and long-acting reversible covalent inhibitors of staphylococcal sortase. The efficacy of sortase inhibition is demonstrated through biochemical and cell-based assays. A comparative study between RMR1 and an iminoboronate-forming warhead emphasizes the importance and potential of modulating bond dissociation kinetics in achieving long-acting reversible covalent inhibitors.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Difei Zhang, Chao Liu, Kaicheng Zhang, Yanhua Jia, Wenkai Zhong, Weidong Qiu, Yuanfeng Li, Thomas Heumueller, Karen Forberich, Vincent M. Le Corre, Larry Lueer, Ning Li, Fei Huang, Christoph J. Brabec, Lei Ying
Summary: Device stability is a crucial obstacle for the industrial application of organic photovoltaics. The study shows that post-thermal annealing can partially recover the light-induced burn-in losses in high-performance organic solar cells, which is correlated with reversible charge extraction ability, trap density of state, local charge carrier density, and charge accumulation. The presence of light-induced long-persistent radicals triggers the degradation process, offering new insights into improving device stability.
ENERGY & ENVIRONMENTAL SCIENCE
(2023)
Article
Materials Science, Multidisciplinary
F. Michael Russell, Juan F. R. Archilla
Summary: Recent developments in hyperconductivity research have reported loss-free transmission of electric charge at room temperature and above, attributed to the ballistic transport of electric charge in crystals with quasi-layered structure. The study introduces the concept of quodons, a type of mobile nonlinear intrinsic localized mode of lattice excitation that carries electric charge and has been observed in layered silicates and laboratory experiments. Only layered silicates have demonstrated hyperconductivity, while new evidence suggests hyperconductivity in nonlayered silicate material chrysotile. Quodons are shown to be able to carry charge in various materials, including polymers, although hyperconductivity is not observed in these materials due to limitations in range and lifetime of quodons.
PHYSICA STATUS SOLIDI-RAPID RESEARCH LETTERS
(2022)
Article
Physics, Multidisciplinary
Faustino Palmero, Mario Molina, Jesus Cuevas-Maraver, Panayotis G. Kevrekidis
Summary: This article extends the study on embedded modes by exploring two directions in the realms of discrete nonlinear Schrodinger and Klein-Gordon settings. It is found that the stability of the modes transitions from stability to instability as nonlinearity surpasses a critical value, leading to a dynamical delocalization of the solitary wave (or breathing) state.
Article
Mathematics
Dirk Hennig, Nikos Karachalios, Jesus Cuevas-Maraver
Summary: This paper proves the similarity in terms of continuous dependence on initial data between the Ablowitz-Ladik lattice system and the Discrete Nonlinear Schrodinger equation, with a particular focus on the persistence of small amplitude solutions of the Ablowitz-Ladik system in the Discrete Nonlinear Schrodinger equation.
JOURNAL OF DIFFERENTIAL EQUATIONS
(2022)
Article
Physics, Mathematical
Dirk Hennig, Nikos Karachalios, Jesus Cuevas-Maraver
Summary: This study proves the closeness between the solutions of the Ablowitz-Ladik system and a class of Discrete Nonlinear Schrödinger systems in terms of continuous dependence on their initial data. It shows that small amplitude waveforms can persist in nonintegrable lattices. Numerical simulations confirm the analytical results, demonstrating the persistence of small amplitude Ablowitz-Ladik solutions in nonintegrable systems.
JOURNAL OF MATHEMATICAL PHYSICS
(2022)
Article
Physics, Multidisciplinary
Atanas Stefanov, Georgios A. Tsolias, Jesus Cuevas-Maraver, Panayotis G. Kevrekidis
Summary: This paper provides a characterization of the ground states of a higher-dimensional quadratic-quartic model and investigates the stability of the system under different parameters. It is found that the stability of the system is influenced within a certain parameter range, and there exists a range of stable frequencies.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Article
Mathematics
Janis Bajars, Juan F. R. Archilla
Summary: In this paper, we propose two classes of symplecticity-preserving splitting methods for charge transfer in nonlinear crystal lattice models. We derive canonical Hamiltonian equations and dispersion relations to construct structure-preserving splitting methods. We also propose symplectic splitting methods that conserve exactly the charge probability. The developed methods are demonstrated numerically using an example model for charge transport.
Article
Physics, Applied
F. Michael Russell, Juan F. R. Archilla
Summary: The history of experimental study on nonlinear lattice excitations in layered silicate materials is briefly described in this article. The term "quodon" was adopted to reflect their ballistic and quasi-one-dimensional propagative nature. Experimental observations of quodons in muscovite revealed that these lattice excitations carry an electric charge. The existence of quodons led to the prediction and subsequent experimental observation of hyperconductivity (HC), where charge is carried ballistically by neutral, mobile lattice excitations at any temperature and in the absence of a driving electromotive force. Practical applications of HC require encasing the HC material in an insulating sheath, which highlighted the behavior of insulating materials in the presence of quodons.
LOW TEMPERATURE PHYSICS
(2022)
Article
Mathematics, Applied
Janis Bajars, Juan F. R. Archilla
Summary: We study the propagation of nonlinear excitations in a hexagonal layer, which serves as a model for the cation layer of silicates. We extend the theory of pterobreathers to two dimensions, considering their properties in the frequency-momentum representation. Exact traveling waves and co-traveling wings with a small set of frequencies are obtained by perturbing the system.
PHYSICA D-NONLINEAR PHENOMENA
(2022)
Article
Mathematics, Applied
Dirk Hennig, Nikos I. Karachalios, Jesus Cuevas-Maraver
Summary: In this work, we prove that dissipative solitonic waveforms persist for significant times in the discrete complex Ginzburg-Landau equation by introducing a dynamical transitivity argument. This argument is based on the inviscid limits and the continuous dependence of solutions on their initial data, establishing closeness between the dissipative system and its Hamiltonian counterparts.
JOURNAL OF NONLINEAR SCIENCE
(2023)
Article
Mathematics, Applied
Juan F. R. Archilla, Janis Bajars
Summary: In this paper, the spectral properties of polarobreathers, breathers carrying charge in a one-dimensional semiclassical model, are studied. The authors employ recently developed numerical methods to preserve the charge probability at each time integration step, without using the Born-Oppenheimer approximation. An algorithm is developed to obtain exact polarobreather solutions. The properties of polarobreathers, both stationary and moving ones, are deduced from the lattice and charge variable spectra in the frequency-momentum space. An efficient approach to produce approximate polarobreathers with long lifespans is considered, and the spectra of exact polarobreathers become simple and easy to interpret. The problem of the non-observable charge frequency is also addressed, with a focus on the observable frequency of the charge probability.
Article
Materials Science, Multidisciplinary
Francis Michael Russell, Juan F. R. Archilla, Jose L. Mas
Summary: Tokamak fusion reactors produce He ions and neutrons that have different penetration abilities. Nonlinear lattice excitations create mobile lattice excitations called quodons, which can couple to and transport electric charge. This article presents an experimental design to separate quodon current and conduction current, and measurements show that many quodons are produced in fusion reactors. It is predicted that quodons may negatively impact cryogenic systems.
PHYSICA STATUS SOLIDI-RAPID RESEARCH LETTERS
(2023)
Article
Physics, Fluids & Plasmas
Ross Parker, Alejandro Aceves, Jesus Cuevas-Maraver, P. G. Kevrekidis
Summary: In this study, we investigate coherent structures in a one-dimensional discrete nonlinear Schrodinger lattice with periodically modulated coupling between waveguides. Numerical experiments reveal two fundamentally different behaviors of the system depending on the power: transport with energy moving unidirectionally for low power, and stationary solutions for high power. By analyzing a simplified model with step functions, we explain these behaviors and the transition between them. We numerically construct stationary and moving coherent structures for the original model, and use Floquet analysis to determine the spectral stability of the stationary solutions. Typically, the traveling solutions exhibit small-amplitude oscillatory tails, although there are parameters for which these tails disappear.
Article
Physics, Fluids & Plasmas
Jesus Cuevas-Maraver, Panayotis G. Kevrekidis, Hong-Kun Zhang
Summary: In this study, we investigate the concept of solitary wave billiards, where a solitary wave is examined within an enclosed region and its collision with boundaries and resulting trajectories are analyzed. It is found that solitary wave billiards are generally chaotic, even in cases where particle billiards are integrable. The level of chaoticity depends on particle speed and potential properties. Additionally, the scattering nature of deformable solitary wave particles is explained based on a negative Goos-Hanchen effect, which leads to both a trajectory shift and effective shrinkage of the billiard domain.
Article
Physics, Fluids & Plasmas
Henry Duran, Jesus Cuevas-Maraver, Panayotis G. Kevrekidis, Anna Vainchtein
Summary: By analyzing the linear band structure of a mechanical metamaterial, we find that discrete breather solutions can exist in certain parameter regimes within the gap between optical and acoustic dispersion bands. Numerical computations reveal the properties and stability of these solutions in different parameter regimes. The study demonstrates that the system exhibits a variety of discrete breathers, including period-doubling, symmetry-breaking bifurcations, and other mechanisms of stability change, which can be explored experimentally.
Article
Physics, Fluids & Plasmas
Ross Parker, Alejandro Aceves, Jesus Cuevas-Maraver, P. G. Kevrekidis
Summary: In this work, a topological two-dimensional lattice with periodically time-dependent interactions is revisited, identifying fundamental solitons and analyzing their Floquet stability. Multisoliton analogs show different stability properties.
