Article
Materials Science, Multidisciplinary
Karol Kawa, Pawel Machnikowski
Summary: In this study, we investigate the spread of correlations in a one-dimensional lattice system with high on-site energy disorder and long-range couplings. We find that the increase in correlation between two nodes exhibits three phases and we also obtain an approximate solution of the model valid in the limit of strong disorder.
Article
Acoustics
Xiang Liu, Guoping Cai, K. W. Wang
Summary: This paper investigates topologically protected wave propagation in metastable structure by mimicking the quantum valley Hall effect, achieving reconfigurable topological waveguides. Through breaking the space inversion symmetry of the unit cell and opening a topological bandgap, the non-triviality of the bandgap is verified using Berry curvature and valley Chern number. Utilizing edge modes, topologically protected waveguides immune to backscattering at sharp corners and local defects are achieved.
JOURNAL OF SOUND AND VIBRATION
(2021)
Article
Multidisciplinary Sciences
Nooshin M. Estakhri, Nasim Mohammadi Estakhri, Theodore B. Norris
Summary: This study develops a scattering model to investigate coherent backscattering cone formation in finite-sized and sparse random media with specific geometries. The results show that density, volume size, and other parameters affect the angular characteristics of the CBS cone, with consistent results compared to previous CBS studies.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Nicholas Bender, Arthur Goetschy, Chia Wei Hsu, Hasan Yilmaz, Pablo Jara Palacios, Alexey Yamilov, Hui Cao
Summary: This study demonstrates that wavefront shaping can enhance the remission of light in diffusive media, with a maximum enhancement of up to 10 transport mean free paths. A theoretical model is developed to predict the maximal remission enhancement, and the analysis shows a significant improvement in the sensitivity of remitted waves to local changes of absorption deep inside diffusive media. These findings illustrate the potential importance of coherent wavefront control in noninvasive imaging applications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Optics
Ivana Kurecic, Tobias J. Osborne
Summary: The dynamics of interacting quantum systems in the presence of disorder is studied and an exact representation for disorder-averaged quantities via Ito stochastic calculus is obtained. The stochastic integral representation allows for analytic approximation, potential applicability to interacting systems, and compatibility with tensor network methods. The integral can be expanded to produce a series of approximations, the first of which includes all diffusive corrections and is manifestly completely positive. As examples, expressions for the density of states and spectral form factor for the Anderson model are obtained.
Article
Optics
Dejan Timotijevic, Jadranka M. Vasiljevic, Dragana M. Jovic Savic
Summary: We have numerically modeled two different methods for randomizing two-dimensional aperiodic photonic lattices based on Mathieu beams induced in a photorefractive media. We compared the light transport and localization in these lattices for different disorder strengths and observed disorder-enhanced light transport for all strengths of disorder. As the disorder strength increased, the light transport became diffusive-like, and further increase led to Anderson localization. This trend was more pronounced for longer propagation distances. We studied the influence of input lattice intensity on the localization effects and attributed the difference in light transport between the two randomization methods to varying levels of input lattice intensity. We observed more pronounced localization for one of the methods, and the localization lengths varied along different directions due to crystal and lattice anisotropy. We analyzed the localization effects by comparing uniform and on-site probe beam excitation positions and different probe beam widths.
Article
Optics
Levi Smith, Walid Gomma, Hadi Esmaeilsabzali, Thomas Darcie
Summary: This paper quantifies the efficacy of transmission-line tapers connecting different coplanar-strip transmission-line configurations, providing important references for the design of terahertz systems.
Article
Chemistry, Physical
Kianoosh Taghizadeh, Rohit Kumar Shrivastava, Stefan Luding
Summary: The study investigates energy transfer in disordered one-dimensional model systems mimicking force-chains in real systems, with pre-stressed random masses interacting through linearized Hertzian repulsive forces. A simpler, faster stochastic model for energy propagation is presented, with focus on pulse propagation in disordered granular chains. Increasing disorder leads to attenuation of pulsed signals, transitioning from ballistic propagation to diffusive-like characteristics, while energy localization at the source is observed. The decay of energy increases with disorder and wavenumber, transitioning from dispersive ballistic transport in ordered systems to low-pass filtering due to disorder.
Article
Optics
Xiaowen Hu, Jian Zhao, Jose Enrique Antonio-Lopez, Rodrigo Amezcua Correa, Axel Schulzgen
Summary: The fusion of fiber-optic imaging with supervised deep learning has seen significant development in recent years, enabling high-quality imaging of difficult-to-reach areas. However, the requirement for paired collection of input objects and fiber outputs limits the potential of fiber-optic imaging. The use of unsupervised image reconstruction, based on transverse Anderson localization in disordered fibers, offers a new solution. In this study, unsupervised full-color imaging with cellular resolution was successfully demonstrated through a meter-long disordered fiber in both transmission and reflection modes. Two stages of unsupervised image reconstruction, involving pixel-wise standardization and fine detail recovery through a generative adversarial network, were employed. This approach allows for flexible calibration under various conditions without the need for paired images.
LIGHT-SCIENCE & APPLICATIONS
(2023)
Article
Astronomy & Astrophysics
Wei-Liang Qian, Kai Lin, Cai-Ying Shao, Bin Wang, Rui-Hong Yue
Summary: The black hole quasinormal modes resulting from a piecewise approximate potential are drastically different from those of the original black hole metric, with the spectrum stretching out along the real axis instead of lining up parallel to the imaginary axis. Even a slight discontinuity in the effective potential significantly modifies the asymptotic behavior of the quasinormal modes, as supported by analytical derivations. Additionally, the astrophysical implications of these findings are discussed.
Article
Physics, Multidisciplinary
Ralf Metzler, Ashish Rajyaguru, Brian Berkowitz
Summary: In this study, we investigate the dynamics of the concentration profile in a one-dimensional, semi-infinite disordered system connected to a reservoir of tracer particles kept at constant concentration. By using the Montroll-Weiss equation and the fractional diffusion equation, we obtain analytical expressions for the concentration profile and derive the tracer flux and breakthrough curve. We demonstrate a long-time power-law behavior for the residual breakthrough curves and compare it with experimental measurements.
NEW JOURNAL OF PHYSICS
(2022)
Article
Computer Science, Interdisciplinary Applications
Jesus Ruano, Aleix Baez Vidal, Joaquim Rigola, Francesc Xavier Trias
Summary: This article presents a new numerical method for analyzing dispersion errors and evaluating them on Cartesian stretched grids for linear advection problems. The spectral properties of several convective schemes, including non-linear ones, are discussed. The results show convergence with classical methods on uniform structured meshes, and the proposed method considers the effects on time step depending on the scheme used, ultimately allowing for the proposal of an optimal scheme based on meshing strategy.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Materials Science, Multidisciplinary
Saumitran Kasturirangan, Alex Kamenev, Fiona J. Burnell
Summary: This study investigates the influence of (chiral) symmetry-preserving disorder on topological multicritical points. It finds that delocalized states with diverging localization length at zero energy exist, consistent with the W=1 critical point. The density of states (DOS) exhibits the universal Dyson singularity, while the critical exponent of the zero-energy localization length depends on the topological index W.
Article
Materials Science, Multidisciplinary
Soumi Ghosh, Sparsh Gupta, Manas Kulkarni
Summary: This study analyzes the chaotic behavior of non-Hermitian interacting disordered Hamiltonians through the non-Hermitian analog of the spectral form factor and the complex spacing ratio. The findings are expected to play a crucial role in understanding disordered open quantum systems in general.
Article
Mathematics, Applied
Risong Li, Tianxiu Lu, Xiaofang Yang, Yongxi Jiang
Summary: In this paper, the concepts of ergodic multi-sensitivity and strongly ergodically multi-sensitivity are introduced, with special cases proven in compact metric spaces. It is also demonstrated how the properties of different spaces and maps are related to each other.
Article
Biochemical Research Methods
Mattia Miotto, Alexandros Armaos, Lorenzo Di Rienzo, Giancarlo Ruocco, Edoardo Milanetti, Gian Gaetano Tartaglia
Summary: In this study, a webserver called Thermometer was developed to assess the thermal stability of proteins using structural information. The server is publicly available and has a user-friendly interface.
Article
Chemistry, Physical
Marco Benedetti, Enrico Ventura, Enzo Marinari, Giancarlo Ruocco, Francesco Zamponi
Summary: This study compares the Hebbian unlearning algorithm with a symmetric perceptron algorithm and finds that they have similar properties in terms of basin size and convergence region. The study also proposes a geometric interpretation of Hebbian unlearning and explores its potential applications in memory storage in materials.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Lorenzo Di Rienzo, Luca De Flaviis, Giancarlo Ruocco, Viola Folli, Edoardo Milanetti
Summary: This study proposes a new computational approach based on Zernike polynomials for identifying binding sites of specific ligands on GPCRs. By analyzing the shape complementarity of local molecular surfaces, the method can distinguish binding pockets from randomly sampled regions on the receptor surface. The method achieves an Area Under ROC curve of 0.77 in experiments, demonstrating its ability for rapid and efficient screening of potential drugs.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Biology
Mattia Miotto, Lorenzo Di Rienzo, Giorgio Gosti, Leonardo Bo', Giacomo Parisi, Roberta Piacentini, Alberto Boffi, Giancarlo Ruocco, Edoardo Milanetti
Summary: The researchers conducted molecular dynamics simulations to assess the stabilizing effect of several possible SARS-CoV-2 spike variants on the molecular complex. They found that several variants exhibited greater stability compared to the wild type and negative control systems. The study highlights the importance of characterizing the effects of these variants' mutations on contagiousness and antigenicity.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Roberta Piacentini, Laura Centi, Mattia Miotto, Edoardo Milanetti, Lorenzo Di Rienzo, Martina Pitea, Paolo Piazza, Giancarlo Ruocco, Alberto Boffi, Giacomo Parisi
Summary: This study investigates the interactions among human lactoferrin, SARS-CoV-2 receptor-binding domain, and human angiotensin-converting enzyme 2 receptor. The results suggest that lactoferrin can bind to ACE2 receptor but not to RBD. This reveals a potential mechanism for lactoferrin's preventive effect against CoV-2 infection by interfering with RBD-ACE2 binding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Manola Moretti, Tania Limongi, Claudia Testi, Edoardo Milanetti, Maria Teresa De Angelis, Elvira I. Parrotta, Stefania Scalise, Gianluca Santamaria, Marco Allione, Sergei Lopatin, Bruno Torre, Peng Zhang, Monica Marini, Gerardo Perozziello, Patrizio Candeloro, Candido Fabrizio Pirri, Giancarlo Ruocco, Giovanni Cuda, Enzo Di Fabrizio
Summary: This study combines transmission electron microscopy, atomic force microscopy, and surface enhanced Raman spectroscopy to gather structural and chemical information of complex molecular systems, such as ion channels, in their original plasma membrane. It identifies the channels using two different approaches and allows a series of complementary investigations on the same sample.
Article
Multidisciplinary Sciences
Elsa Zacco, Owen Kantelberg, Edoardo Milanetti, Alexandros Armaos, Francesco Paolo Panei, Jenna Gregory, Kiani Jeacock, David J. Clarke, Siddharthan Chandran, Giancarlo Ruocco, Stefano Gustincich, Mathew H. Horrocks, Annalisa Pastore, Gian Gaetano Tartaglia
Summary: In this study, aptamers specific for Amyotrophic Lateral Sclerosis protein TDP-43 were successfully designed and used to track TDP-43 phase transition in vitro and in cells.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Fausta Desantis, Mattia Miotto, Lorenzo Di Rienzo, Edoardo Milanetti, Giancarlo Ruocco
Summary: This article investigates the molecular determinants of protein-protein binding affinity and compares them with the factors regulating fold stability. The study finds that Coulombic interactions are correlated with protein thermal stability, while van der Waals energies are correlated with protein-protein binding affinity. Hydrophobic residues are preferentially located in the binding regions, while charged residues behave oppositely. The study also introduces a method to rapidly and accurately predict and design optimal binding regions based on shape complementarity.
SCIENTIFIC REPORTS
(2022)
Article
Materials Science, Multidisciplinary
Martina Marcotulli, Maria Celeste Tirelli, Marina Volpi, Jakub Jaroszewicz, Chiara Scognamiglio, Piotr Kasprzycki, Karol Karnowski, Wojciech Swieszkowski, Giancarlo Ruocco, Marco Costantini, Gianluca Cidonio, Andrea Barbetta
Summary: 3D printing systems have evolved greatly in the last decade, becoming a top technology for academic and industrial applications. However, manufacturing polymeric materials with trabecular porosity and functionally graded architecture through additive platforms remains a technical challenge. This study presents a 3D extrusion printing strategy that enables the construction of high-accuracy polymeric foams with varying density and composition.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Review
Cell Biology
Ilaria Genovese, Ersilia Fornetti, Giancarlo Ruocco
Summary: The relationships between mitochondria, ER, and lysosomes play a crucial role in cell homeostasis regulation and stress response. Protein aggregation can lead to cellular damage and stress. This review summarizes the complex liaison between mitochondria, ER, and lysosomes, with a particular focus on their role in cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Physical
My Nguyen, Kevin Shen, Nicholas Sherck, Stephan Koehler, Rohini Gupta, Kris T. Delaney, M. Scott Shell, Glenn H. Fredrickson
Summary: This study examines the self-assembly and phase separation of polyelectrolyte-surfactant mixtures and their importance in various applications, such as personal care products and drug encapsulation. The researchers investigate how the morphology of micelles and degree of polyelectrolyte adsorption change with varying surfactant mixing ratios and the inclusion of nonionic surfactants. Using molecularly informed field theories constructed from all-atom simulations, they find that the size and surface charge of micelles can be modulated, affecting the degree of polyelectrolyte adsorption, which aligns with experimental observations.
EUROPEAN PHYSICAL JOURNAL E
(2023)
Article
Biochemical Research Methods
Riccardo Reale, Giovanna Peruzzi, Maryamsadat Ghoreishi, Helena Stabile, Giancarlo Ruocco, Marco Leonetti
Summary: This article introduces a microfluidic scanning flow cytometer (mu SFC) that can achieve accurate angle-resolved scattering measurements within a standard polydimethylsiloxane microfluidic chip. In contrast to conventional flow cytometers and fluorescence activated cell sorters, the mu SFC yields linearly correlated size estimates and quantitative refractive index estimates for particles, making it suitable for characterizing biological samples and potentially applicable in diagnostic settings.
Article
Multidisciplinary Sciences
N. Shashaank, Mahalakshmi Somayaji, Mattia Miotto, Eugene V. Mosharov, Emily A. Makowicz, David A. Knowles, Giancarlo Ruocco, David L. Sulzer
Summary: Dopamine neurotransmission in the striatum plays a crucial role in normal and disease functions. This study utilizes computational models to analyze fast-scan cyclic voltammetry recordings in mice and provides insight into the modulation of dopamine release and reuptake. The findings support previous research and reveal the involvement of synuclein proteins in dopamine neurotransmission.
Article
Materials Science, Multidisciplinary
Taras Bryk, Noel Jakse, Giancarlo Ruocco, Jean-Francois Wax
Summary: We present a combined theoretical and simulation study on collective excitations in the three-component metallic glass Zr46Cu46Al8. We demonstrate how partial current time correlation functions can be used to represent them via total mass and mass-concentration currents, describing hydrodynamic acoustic and nonhydrodynamic opticlike modes separately in the long-wavelength region. We provide dispersions of acoustic and optic modes over a wide range of wave numbers and analyze the dispersion and damping of three transverse short-wavelength modes, which helps to interpret existing experimental data accurately.
Meeting Abstract
Cell & Tissue Engineering
Gianluca Cidonio, Federico Salaris, Janos Kanczler, Alessandro Soloperto, Chiara Scognamiglio, Andrea Barbetta, Jonathan Dawson, Richard Oreffo, Alessandro Rosa, Giancarlo Ruocco
TISSUE ENGINEERING PART A
(2022)