arXiv subjects

Xubiao Peng

Publications and source records attributed to Xubiao Peng.

At least 19 recordsLinked to original sources

arXiv2025

Ultrasensitive Label-free Detection of Human CEACAM5 using a WGM Resonator Based on Thin-walled Capillary

Whispering gallery mode (WGM) laser sensors, utilizing the interaction between the in-plane evanescent field and the surface vicinity, provide enhanced sensitivity in label-free sensing for bioanalysis and disease screening. However, the unavoidably excited spiral modes resulting from the weak axial confinement and their sensing potential were overlooked. In this study, a microfluidic biosensor using the localized conical modes of an active resonator based on the thin-walled capillaries was developed, demonstrating ultrasensitive refractive index and biomolecule detection capabilities. This sensor provides nonspecific detection of bovine serum albumin (BSA) and specific detection of Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) with ultra-low detection limits, large sensing range, rapid response, and a cost-effective design, making it a promising candidate for industrial-scale production. The theoretical detection limit for CEACAM5 is as low as 0.38ag/mL (5zM), and the sensitivity in the linear region reaches 0.25nm/(ag/mL). These results are approximately an order of magnitude higher in sensitivity than currently reported active WGM biosensors, demonstrating enormous detection potential for biomarkers.

physics.optics↗

arXiv2023

Ultra-low threshold pH sensor based on a whispering gallery mode microbubble resonator

Laser sensing has a wide range of applications. In this paper, we propose a pH sensing laser with an ultra-low threshold and low sample consumption based on a whispering-gallery-mode microbubble resonator. Rhodamine 6G aqueous solutions with different pH values are used as the lasing gain media, which are injected through the microfluidic channel and interact with the high-quality-factor microbubble resonator to achieve lasing. Subtle pH changes of the aqueous solution lead to changes in lasing intensity in real time and the threshold reaches a minimum of 0.091 uJ/mm2. The low pump energy density effectively avoids the self-aggregation and photobleaching effects of dye molecules present in high-concentration rhodamine 6G solutions. The lasing characteristics under different pH conditions were determined experimentally and theoretically, and the results are in good agreement. Due to the deprotonation of amino groups in highly alkaline environments, the lasing threshold is highly dependent on the pH of rhodamine 6G aqueous solutions. In the pH range of 10.16-13.14, the lasing intensity changes considerably with the increasing pH. The proposed pH-sensing laser exhibits a fast response time, low toxicity, and a high signal-to-noise ratio, making it promising for highly sensitive alkaline detection in biological applications.

physics.optics↗

arXiv2023

From Feynman's ratchet to timecrystalline molecular motors

Cats use the connection governing parallel transport in the space of shapes to land safely on their feet. Here we argue that this connection also explains the impressive performance of molecular motors by enabling molecules to evade conclusions of Feynman's ratchet-and-pawl analysis. We first demonstrate, using simple molecular models, how directed rotational motion can emerge from shape changes even without angular momentum. We then computationally design knotted polyalanine molecules and show how their shape space connection organizes individual atom thermal vibrations into collective rotational motion, independently of angular momentum. Our simulations show that rotational motion arises effortlessly even in ambient water, making the molecule an effective theory time crystal. Our findings have potential for practical molecular motor design and engineering and can be verified through high-precision nuclear magnetic resonance measurements.

cond-mat.soft↗

arXiv2023

Research on the transition dynamics and linear (nonlinear) optical properties of mCherry

In this study, we explore the electron transition mechanism and optical properties of the popular red fluorescent protein mCherry. By examining the charge transfer spectrum and combining it with the mCherry hole-electron distribution, we identify that the charge transfer between the phenolate and imidazolinone loops significantly contributes to the absorption spectrum. Quantitative analysis of charge transfer shows that, overall, the electrons are transferred to the C16 atom in the middle of phenolate and the imidazolinone loops during absorption. We speculate that C16 may also absorb protons to enable the photoconversion of mCherry in the excited state, similar to the blinking mechanism of IrisFP. In addition, we further investigated the optical properties of mcherry in the external field by polarizability (hyperpolarizability), showing the anisotropy of the polarization, the first hyperpolarization and the second hyperpolarization by unit spherical representation. Our results suggest that significant polarization and second hyperpolarizability occur when the field direction and electron transfer direction are aligned. We also analyzed the polarizability and first hyperpolarizabilities for different external fields. The polarizability mutated when the external field satisfies the S_0,min-> S_1 transition. Finally, the study of the first hyperpolarizability shows that adjusting the appropriate field can lead to a linear photoelectric effect or second harmonic generation of mCherry. These studies have certain reference values for various red fluorescent protein correlation simulations and experiments because of the similarity of the red fluorescent protein.

physics.chem-ph↗

arXiv2023

An mCherry biolaser based on microbubble cavity with ultra-low threshold

Biolasers show considerable potential in the biomedical field. Fluorescent protein (FP) is a type of biomaterial with good luminescence efficiency that can be used as the luminescent gain medium in biolasers. Due to the higher cell/tissue permeability, lower cell phototoxicity, and relatively less background fluorescence than other fluorescent proteins, the red fluorescent protein is more suitable in biological applications. MCherry is the most extensively used high-quality red fluorescent protein because of its short maturation time and stable luminescence properties. In this study, using mCherry and microbubble cavity, we realize a highly stable mCherry fluorescent protein laser. The laser resonator achieves a quality factor of 10^8, which is the highest Q factor among the currently available FP lasers. Moreover, this laser exhibits low threshold of 286 fJ, which can effectively protect the luminescent material from being damaged by pump light. Such a threshold is the lowest in the FP lasers as per our knowledge. The prepared laser shows excellent stability in a wide pH range with good photobleaching resistance and can be stored at 4 degree for nearly a month. Also, the laser can serve as a high-sensitivity molecular concentration detector with mCherry as biomarker, owing to its lasing threshold behavior.

physics.optics↗

arXiv2022

Wafer-level substrate-free low-stress silicon nitride platform for THz metadevices and monolithically integrated narrowband metamaterial absorbers

The implementation of terahertz (THz) wafer-level metadevices is critical to advance the science for applications including (I) integrated focal plane array which can image for biology and (II) integrated narrowband absorbers for high spectral resolution THz spectroscopy. Substantial progress has been made in the development of THz metamaterials; however, a wafer-level low-stress THz metadevices platform remains a challenge. This paper experimentally demonstrates a substrate-free THz metadevices platform adopting engineered Si-rich and low-stress silicon nitride (SiNx) thin films, achieving an extensive THz transparency up to f = 2.5 THz. A new analytical model is first reported from the Lorentz model that can accurately predict spectral responses of metal insulator metal (MIM) metamaterial absorbers. The model is experimentally validated in the THz range and exploited for the first demonstration of a THz absorber, which exhibits performance approaching the predicted results. Our results show that the wafer-level SiNx platform will accelerate the development of large-scale, sophisticated substrate-free THz metadevices. The Lorentz model and its quadratic model will be a very practical method for designing THz metadevices.

physics.optics↗

arXiv2022

MD simulations and experiments of plasma proteins adsorption to the biodegradable magnesium alloys to facilitate cell response

Once the magnesium alloy was implanted in the body, it was immediately covered with plasma proteins. The coated alloy surface promoted the adsorption and growth of osteoblasts. Herein, in vitro biological reactions of the ZK60 and AZ31 magnesium alloys were analyzed with and without plasma proteins incubation. The plasma proteins adsorbed on the magnesium alloy were characterized using mass spectrometry (MS). The MS results show that proteins related to bone cells such as fibrinogen, vitronectin, fibronectin, and prothrombin are prone to adsorbed on the surface of the alloys than other proteins. These proteins restrain the degradation of Mg alloys and promote the adsorption and growth of bone cells, which demonstrated by the immersion tests and biocompatibility assays. Furthermore, molecular dynamics simulations were used to analyze the details of the adsorptions of fibrinogen, fibronectin, and prothrombin on ZK60 and AZ31at atomic level. It is revealed that the type of residues adsorbed on the surface of the material has an important effect on protein adsorption.

physics.bio-ph↗

arXiv2022

Ultralow-threshold green fluorescent protein laser based on high Q microbubble resonators

Biological lasers have attracted vast attention because of their potential medical application prospects, especially the low threshold biological laser, which can be used for ultrasensitive biological detection while ensuring that its luminous gain medium is not damaged by the high-energy pump light. By coupling the low concentration green fluorescent protein (GFP) solution with a high Q whispering gallery mode microbubble resonator, we managed to fabricate a miniature GFP laser with ultralow lasing threshold of 500 nJ/mm^2. The energy used to excite the GFP can be reduced to 380 fJ, two orders of magnitude lower than that of the lowest excitation energy GFP laser known. The Q value of the optical cavity in this biological laser is 5.3 x 10^7, the highest among GFP lasers at present. We further confirmed the long-term stability of the working characteristics of GFP laser for the first time and found that its optical characteristics can be maintained for at least 23 days. Finally, we measured the effects of different concentrations of fluorescent protein on the laser threshold. The data show that this biological laser can be used for a highly sensitive detection of GFP concentration.

physics.optics↗

arXiv2021

Field-effect at electrical contacts to two-dimensional materials

The inferior electrical contact to two-dimensional (2D) materials is a critical challenge for their application in post-silicon very large-scale integrated circuits. Electrical contacts were generally related to their resistive effect, quantified as contact resistance. With a systematic investigation, this work demonstrates a capacitive metal-insulator-semiconductor (MIS) field-effect at the electrical contacts to 2D materials: the field-effect depletes or accumulates charge carriers, redistributes the voltage potential, and give rise to abnormal current saturation and nonlinearity. On the one hand, the current saturation hinders the devices' driving ability, which can be eliminated with carefully engineered contact configurations. On the other hand, by introducing the nonlinearity to monolithic analog artificial neural network circuits, the circuits' perception ability can be significantly enhanced, as evidenced using a COVID-19 critical illness prediction model. This work provides a comprehension of the field-effect at the electrical contacts to 2D materials, which is fundamental to the design, simulation, and fabrication of electronics based on 2D material.

physics.app-ph↗

arXiv2020

Substrate-free THz focal plane metamaterial array with high absorption ratio

Microelectromechanical system (MEMS) focal plane array (FPA) with optical readout offers exciting opportunities for real-time terahertz (THz) imaging. However, conventional FPA suffers from a low THz absorption ratio, which further decreases the performance of THz imaging. Here, we present a simple and scalable approach for the realization of THz focal plane metamaterial array with a relatively high absorption ratio. The key idea is to combine the advantages of substrate-free structures with metamaterial. A 100 x100 THz FPA with a 150 x 150 μm pixel is designed, fabricated, and characterized. The dependence of the THz absorption ratio on the thickness of SiNx dielectric substrate film is investigated. The fabricated FPA exhibits a 90.6% resonant absorption at 1.36 THz, agreeing considerably with the theoretical simulation results. Our results imply that such a substrate-free THz focal plane metamaterial array enables the realization of THz imaging.

physics.app-ph↗

arXiv2020

Rotation by shape change, autonomous molecular motors and effective timecrystalline dynamics

A deformable body can rotate even with no angular momentum, simply by changing its shape. A good example is a falling cat, how it maneuvers in air to land on its feet. Here a first principles molecular level example of the phenomenon is presented. For this the thermal vibrations of individual atoms in an isolated cyclopropane molecule are simulated in vacuum and at ultralow internal temperature values, and the ensuing molecular motion is followed stroboscopically. It is observed that in the limit of long stroboscopic time steps the vibrations combine into an apparent uniform rotation of the entire molecule even in the absence of angular momentum. This large time scale rotational motion is then modeled in an effective theory approach, in terms of timecrystalline Hamiltonian dynamics. The phenomenon is a temperature sensitive measurable. As such it has potential applications that range from models of autonomous molecular motors to development of molecular level detector, sensor and control technologies.

physics.comp-ph↗

arXiv2020

Classical Hamiltonian Time Crystals -- General Theory And Simple Examples

We focus on a Hamiltonian system with a continuous symmetry, and dynamics that takes place on a presymplectic manifold. We explain how the symmetry can become spontaneously broken by a time crystal, that we define as the minimum of the available mechanical free energy that is simultaneously a time dependent solution of Hamilton's equation. The mathematical description of such a timecrystalline spontaneous symmetry breaking builds on concepts of equivariant Morse theory in the space of Hamiltonian flows. As an example we analyze a general family of timecrystalline Hamiltonians that is designed to model polygonal, piecewise linear closed strings. The vertices correspond to the locations of pointlike interaction centers; the string is akin a chain of atoms, that are joined together by covalent bonds, modeled by the links of the string. We argue that the timecrystalline character of the string can be affected by its topology. For this we show that a knotty string is usually more timecrystalline than a string with no self-entanglement. We also reveal a relation between phase space topology and the occurrence of timecrystalline dynamics. For this we show that in the case of three point particles, the presence of a time crystal can relate to a Dirac monopole that resides in the phase space. Our results propose that physical examples of Hamiltonian time crystals can be realized in terms of closed, knotted molecular rings.

nlin.PS↗

arXiv2020

The photon vortex beam in rotating medium

In this paper we consider the photon vortex beam in the rotating medium, where the rotating velocity acts as an effective vector potential. Using the Riemann-Silberstein vector, we construct the photon wave function. Using the Maxwell equations and the first-order Minkowski constitutive relations we get the dynamic equations of photon in moving medium. For the stationary states, the dynamic equations can be written as a Dirac-like equation. We obtain the approximate photon vortex beam solutions by the given the medium's different velocity distribution and find the diffracting and nondiffracting Laguerre-Gaussian beam solutions in the rotating medium. For the diffracting Laguerre-Gaussian beams, we acquire new terms arising from the rotation that can change the Gouy phase, and then accordingly infer the rotation behavior of the photon interference pattern. Furthermore, in our theory we obtain the Landau levels structure of transverse photon energy in the nondiffracting Laguerre-Gaussian beam solutions.

physics.optics↗

arXiv2019

Topologically enhanced time crystals and molecular knots

A time crystal is a time dependent physical system that does not reach a standstill, even in state of minimum energy. Here we show that the stability of a time crystal can be enhanced by its topology. For this we simulate time crystals made of chainlike ensembles of mutually interacting point particles. When we tie the chain into a knot we find that its timecrystalline qualities improve. The theoretical models we consider are widely used in coarse grained descriptions of linear polymers. Thus we expect that physical realizations of time crystals can be found in terms of knotted molecules.

nlin.PS↗

arXiv2019

Improvement in corrosion resistance and biocompatibility of AZ31 magnesium alloy by NH+2 ions

Magnesium alloys have been considered to be favorable biodegradable metallic materials used in orthopedic and cardiovascular applications. We introduce NH+2 to the AZ31 Mg alloy surface by ion implantation at the energy of 50 KeV with doses ranging from 1e16 ions/cm2 to 1e17 ions/cm2 to improve its corrosion resistance and biocompatibility. Surface morphology, mechanical properties, corrosion behavior and biocompatibility are studied in the experiments. The analysis confirms that the modified surface with smoothness and hydrophobicity significantly improves the corrosion resistance and biocompatibility while maintaining the mechanical property of the alloy.

physics.app-ph↗

arXiv2019

Can all-atom protein dynamics be reconstructed from the knowledge of C-alpha time evolution?

We inquire to what extent protein peptide plane and side chain dynamics can be reconstructed from knowledge of C-alpha dynamics. Due to lack of experimental data we analyze all atom molecular dynamics trajectories from Anton supercomputer, and for clarity we limit our attention to the peptide plane O atoms and side chain C-beta atoms. We try and reconstruct their dynamics using four different approaches. Three of these are the publicly available reconstruction programs Pulchra, Remo Scwrl4. The fourth, Statistical Method, builds entirely on statistical analysis of Protein Data Bank (PDB) structures. All four methods place the O and C-beta atoms accurately along the Anton trajectories. However, the Statistical Method performs best. The results suggest that under physiological conditions, the all atom dynamics is slaved to that of C-alpha atoms. The results can help improve all atom force fields, and advance reconstruction and refinement methods for reduced protein structures. The results provide impetus for development of effective coarse grained force fields in terms of reduced coordinates.

q-bio.BM↗

arXiv2018

Truncated Dynamics, Ring Molecules and Mechanical Time Crystals

In applications of mechanics, including quantum mechanics, we often consider complex systems, where complete solutions of the underlying "fundamental" equations is both impractical and unnecessary to describe appropriate observations accurately. For example, practical chemistry, including even precision first-principles quantum chemistry, is never concerned with the behavior of the subnuclear quarks and gluons. Instead, we often focus on a few key variables, and construct a so-called effective theory for those. Such effective theories can become complicated and non-local, even for fairly simple systems. But in many circumstances, when there is a separation of scales, we can treat the reduced set of variables as a conventional dynamical system in its own right, governed by an energy conserving Lagrangian or Hamiltonian, in a useful approximation. The structure of that emergent description can display qualitatively new features, notably including reduced dimensionality, manifested through unconventional Poisson brackets. Here we discuss the physical meaning and consequences of such truncated dynamics. We propose physically realizable toy models of molecular rings, wherein time crystals emerge at the classical level. We propose that such behavior occurs in the effective theory of highly diamagnetic aromatic ring molecules, and could be widespread.

physics.class-ph↗

arXiv2017

Virtual reality analysis of intrinsic protein geometry with applications to cis peptide planes

A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is conventionally characterised by the extrinsically determined Ramachandran angles. However, a protein backbone has also two independent intrinsic geometric structures, due to the peptide planes and the side chains. Here we adapt and develop modern 3D virtual reality techniques to scrutinize the atomic geometry along a protein backbone, in the vicinity of a peptide plane. For this we compare backbone geometry-based (extrinsic) and structure-based (intrinsic) coordinate systems, and as an example we inspect the trans and cis peptide planes. We reveal systematics in the way how a cis peptide plane deforms the neighbouring atomic geometry, and we develop a virtual reality based visual methodology that can identify the presence of a cis peptide plane from the arrangement of atoms in its vicinity. Our approach can easily detect exceptionally placed atoms in crystallographic structures. Thus it can be employed as a powerful visual refinement tool which is applicable also in the case when resolution of the protein structure is limited and whenever refinement is needed. As concrete examples we identify a number of crystallographic protein structures in Protein Data Bank (PDB) that display exceptional atomic positions around their cis peptide planes.

q-bio.BM↗