A new six-component super soliton hierarchy and its self-consistent sources and conservation laws
Denoising of chaotic signal using independent component analysis and empirical mode decomposition with circulate translating
Birkhoffian symplectic algorithms derived from Hamiltonian symplectic algorithms
Atomic-scale simulations of material behaviors and tribology properties for BCC metal film
This work has two main purposes: (i) introducing the basic concepts of molecular dynamics analysis to material scientists and engineers, and (ii) providing a better understanding of instrumented indentation measurements, presenting an example of nanoindentation and scratch test simulations. To reach these purposes, three-dimensional molecular dynamics (MD) simulations of nanoindentation and scratch test technique were carried out for generic thin films that present BCC crystalline structures. Structures were oriented in the plane (100) and placed on FCC diamond substrates. A pair wise potential was employed to simulate the interaction between atoms of each layer and a repulsive radial potential was used to represent a spherical tip indenting the sample. Mechanical properties of this generic material were obtained by varying the indentation depth and dissociation energy. The load-unload curves and coefficient of friction were found for each test; on the other hand, dissociation energy was varied showing a better mechanical response for films that present grater dissociation energy. Structural change evolution was observed presenting vacancies and slips as the depth was varied.
Multi-symplectic variational integrators for nonlinear Schrödinger equations with variable coefficients
Solution of Dirac equation for Eckart potential and trigonometric Manning Rosen potential using asymptotic iteration method
Spin dynamics of the potassium magnetometer in spin-exchange relaxation free regime Hot!
The laser-pumped potassium spin-exchange relaxation free (SERF) magnetometer is the most sensitive detector of magnetic field and has many important applications. We present the experimental results of our potassium SERF magnetometer. A pump-probe approach is used to identify the unique spin dynamics of the atomic ensemble in the SERF regime. A single channel sensitivity of 8 f· THz-1/2 is achieved with our SERF magnetometer.
Entanglement and non-Markovianity of a multi-level atom decaying in a cavity
Tunable ponderomotive squeezing induced by Coulomb interaction in an optomechanical system
Passive decoy-state quantum key distribution for the weak coherent photon source with finite-length key
Detection efficiency characteristics of free-running InGaAs/InP single photon detector using passive quenching active reset IC
Effects of a finite number of particles on the thermodynamic properties of a harmonically trapped ideal charged Bose gas in a constant magnetic field
We investigate the thermodynamic properties of an ideal charged Bose gas confined in an anisotropic harmonic potential and a constant magnetic field. Using an accurate density of states, we calculate analytically the thermodynamic potential and consequently various intriguing thermodynamic properties, including the Bose-Einstein transition temperature, the specific heat, magnetization, and the corrections to these quantities due to the finite number of particles are also given explicitly. In contrast to the infinite number of particles scenarios, we show that those thermodynamic properties, particularly the Bose-Einstein transition temperature depends upon the strength of the magnetic field due to the finiteness of the particle numbers, and the collective effects of a finite number of particles become larger when the particle number decreases. Moreover, the magnetization varies with the temperature due to the finiteness of the particle number while it keeps invariant in the thermodynamic limit N→∞.
Quantum walks with coins undergoing different quantum noisy channels
Quantum walks have significantly different properties compared to classical random walks, which have potential applications in quantum computation and quantum simulation. We study Hadamard quantum walks with coins undergoing different quantum noisy channels and deduce the analytical expressions of the first two moments of position in the long-time limit. Numerical simulations have been done, the results are compared with the analytical results, and they match extremely well. We show that the variance of the position distributions of the walks grows linearly with time when enough steps are taken and the linear coefficient is affected by the strength of the quantum noisy channels.
Complex dynamics of an archetypal self-excited SD oscillator driven by moving belt friction
We propose an archetypal self-excited system driven by moving belt friction, which is constructed with the smooth and discontinuous (SD) oscillator proposed by the Cao et al. and the classical moving belt. The moving belt friction is modeled as the Coulomb friction to formulate the mathematical model of the proposed self-excited SD oscillator. The equilibrium states of the unperturbed system are obtained to show the complex equilibrium bifurcations. Phase portraits are depicted to present the hyperbolic structure transition, the multiple stick regions, and the friction-induced asymmetry phenomena. The numerical simulations are carried out to demonstrate the friction-induced vibration of multiple stick-slip phenomena and the stick-slip chaos in the perturbed self-excited system. The results presented here provide an opportunity for us to get insight into the mechanism of the complex friction-induced nonlinear dynamics in mechanical engineering and geography.
Memcapacitor model and its application in a chaotic oscillator
Effects of abnormal excitation on the dynamics of spiral waves
Parrondo's paradox for chaos control and anticontrol of fractional-order systems
We present the generalized forms of Parrondo's paradox existing in fractional-order nonlinear systems. The generalization is implemented by applying a parameter switching (PS) algorithm to the corresponding initial value problems associated with the fractional-order nonlinear systems. The PS algorithm switches a system parameter within a specific set of N≥2 values when solving the system with some numerical integration method. It is proven that any attractor of the concerned system can be approximated numerically. By replacing the words “winning” and “loosing” in the classical Parrondo's paradox with “order” and “chaos”, respectively, the PS algorithm leads to the generalized Parrondo's paradox: chaos1+chaos2+…+chaosN=order and order1+order2+…+orderN=chaos. Finally, the concept is well demonstrated with the results based on the fractional-order Chen system.
The Wronskian technique for nonlinear evolution equations
Kuznetsov-Ma soliton and Akhmediev breather of higher-order nonlinear Schrödinger equation
In terms of Darboux transformation, we have exactly solved the higher-order nonlinear Schrödinger equation that describes the propagation of ultrashort optical pulses in optical fibers. We discuss the modulation instability (MI) process in detail and find that the higher-order term has no effect on the MI condition. Under different conditions, we obtain Kuznetsov-Ma soliton and Akhmediev breather solutions of higher-order nonlinear Schrödinger equation. The former describes the propagation of a bright pulse on a continuous wave background in the presence of higher-order effects and the soliton's peak position is shifted owing to the presence of a nonvanishing background, while the latter implies the modulation instability process that can be used in practice to produce a train of ultrashort optical soliton pulses.
Study on bi-directional pedestrian movement using ant algorithms
Entropy and heat generation of lithium cells/batteries
The methods and techniques commonly used in investigating the change of entropy and heat generation in Li cells/batteries are introduced, as are the measurements, calculations and purposes. The changes of entropy and heat generation are concomitant with the use of Li cells/batteries. In order to improve the management and the application of Li cells/batteries, especially for large scale power batteries, the quantitative investigations of the change of entropy and heat generating are necessary.
Mechanics of high-capacity electrodes in lithium-ion batteries
Rechargeable batteries, such as lithium-ion batteries, play an important role in the emerging sustainable energy landscape. Mechanical degradation and resulting capacity fade in high-capacity electrode materials critically hinder their use in high-performance lithium-ion batteries. This paper presents an overview of recent advances in understanding the electrochemically-induced mechanical behavior of the electrode materials in lithium-ion batteries. Particular emphasis is placed on stress generation and facture in high-capacity anode materials such as silicon. Finally, we identify several important unresolved issues for future research.
Li-ion batteries: Phase transition
Progress in the research on phase transitions during Li+ extraction/insertion processes in typical battery materials is summarized as examples to illustrate the significance of understanding phase transition phenomena in Li-ion batteries. Physical phenomena such as phase transitions (and resultant phase diagrams) are often observed in Li-ion battery research and already play an important role in promoting Li-ion battery technology. For example, the phase transitions during Li+ insertion/extraction are highly relevant to the thermodynamics and kinetics of Li-ion batteries, and even physical characteristics such as specific energy, power density, volume variation, and safety-related properties.
Soft x-ray spectroscopy for probing electronic and chemical states of battery materials
The formidable challenge of developing high-performance battery system stems from the complication of battery operations, both mechanically and electronically. In the electrodes and at the electrode-electrolyte interfaces, chemical reactions take place with evolving electron states. In addition to the extensive studies of material synthesis, electrochemical, structural, and mechanical properties, soft x-ray spectroscopy provides unique opportunities for revealing the critical electron states in batteries. This review discusses some of the recent soft x-ray spectroscopic results on battery binder, transition-metal based positive electrodes, and the solid-electrolyte-interphase. By virtue of soft x-ray's sensitivity to electron states, the electronic property, the redox during electrochemical operations, and the chemical species of the interphases could be fingerprinted by soft x-ray spectroscopy. Understanding and innovating battery technologies need a multimodal approach, and soft x-ray spectroscopy is one of the incisive tools to probe the chemical and physical evolutions in batteries.
Electrochromic & magnetic properties of electrode materials for lithium ion batteries
Progress in electrochromic lithium ion batteries (LIBs) is reviewed, highlighting advances and possible research directions. Methods for using the LIB electrode materials' magnetic properties are also described, using several examples. Li4Ti5O12 (LTO) film is discussed as an electrochromic material and insertion compound. The opto-electrical properties of the LTO film have been characterized by electrical measurements and UV-Vis spectra. A prototype bi-functional electrochromic LIB, incorporating LTO as both electrochromic layer and anode, has also been characterized by charge-discharge measurements and UV-Vis transmittance. The results show that the bi-functional electrochromic LIB prototype works well. Magnetic measurement has proven to be a powerful tool to evaluate the quality of electrode materials. We introduce briefly the magnetism of solids in general, and then discuss the magnetic characteristics of layered oxides, spinel oxides, olivine phosphate LiFePO4, and Nasicon-type Li3Fe2(PO4)3. We also discuss what kind of impurities can be detected, which will guide us to fabricate high quality films and high performance devices.
Interfacial transport in lithium-ion conductors
Physical models of ion diffusion at different interfaces are reviewed. The use of impedance spectroscopy (IS), nuclear magnetic resonance (NMR), and secondary ion mass spectrometry (SIMS) techniques are also discussed. The diffusion of ions is fundamental to the operation of lithium-ion batteries, taking place not only within the grains but also across different interfaces. Interfacial ion transport usually contributes to the majority of the resistance in lithium-ion batteries. A greater understanding of the interfacial diffusion of ions is crucial to improving battery performance.
Size effects in lithium ion batteries
Size-related properties of novel lithium battery materials, arising from kinetics, thermodynamics, and newly discovered lithium storage mechanisms, are reviewed. Complementary experimental and computational investigations of the use of the size effects to modify electrodes and electrolytes for lithium ion batteries are enumerated and discussed together. Size differences in the materials in lithium ion batteries lead to a variety of exciting phenomena. Smaller-particle materials with highly connective interfaces and reduced diffusion paths exhibit higher rate performance than the corresponding bulk materials. The thermodynamics is also changed by the higher surface energy of smaller particles, affecting, for example, secondary surface reactions, lattice parameter, voltage, and the phase transformation mechanism. Newly discovered lithium storage mechanisms that result in superior storage capacity are also briefly highlighted.
Understanding oxygen reactions in aprotic Li-O2 batteries
Although significant progress has been made in many aspects of the emerging aprotic Li-O2 battery system, an in-depth understanding of the oxygen reactions is still underway. The oxygen reactions occurring in the positive electrode distinguish Li-O2 batteries from the conventional Li-ion cells and play a crucial role in the Li-O2 cell's performance (capacity, rate capability, and cycle life). Recent advances in fundamental studies of oxygen reactions in aprotic Li-O2 batteries are reviewed, including the reaction route, kinetics, morphological evolution of Li2O2, and charge transport within Li2O2. Prospects are also provided for future fundamental investigations of Li-O2 chemistry.
Strategies to curb structural changes of lithium/transition metal oxide cathode materials & the changes' effects on thermal & cycling stability
Structural transformation behaviors of several typical oxide cathode materials during a heating process are reviewed in detail to provide in-depth understanding of the key factors governing the thermal stability of these materials. We also discuss applying the information about heat induced structural evolution in the study of electrochemically induced structural changes. All these discussions are expected to provide valuable insights for designing oxide cathode materials with significantly improved structural stability for safe, long-life lithium ion batteries, as the safety of lithium-ion batteries is a critical issue; it is widely accepted that the thermal instability of the cathodes is one of the most critical factors in thermal runaway and related safety problems.
Physics of electron and lithium-ion transport in electrode materials for Li-ion batteries
The physics of ionic and electrical conduction at electrode materials of lithium-ion batteries (LIBs) are briefly summarized here, besides, we review the current research on ionic and electrical conduction in electrode material incorporating experimental and simulation studies. Commercial LIBs have been widely used in portable electronic devices and are now developed for large-scale applications in hybrid electric vehicles (HEV) and stationary distributed power stations. However, due to the physical limits of the materials, the overall performance of today's LIBs does not meet all the requirements for future applications, and the transport problem has been one of the main barriers to further improvement. The electron and Li-ion transport behaviors are important in determining the rate capacity of LIBs.
Wavy structures for stretchable energy storage devices: Structural design and implementation
The application of wavy structures in stretchable electrochemical energy storage devices is reviewed. First, the mechanical analysis of wavy structures, specific to flexible electronics, is introduced. Second, stretchable electrochemical energy storage devices with wavy structures are discussed. Finally, the present problems and challenges are reviewed, and possible directions for future research are outlined.
High-throughput theoretical design of lithium battery materials
The rapid evolution of high-throughput theoretical design schemes to discover new lithium battery materials is reviewed, including high-capacity cathodes, low-strain cathodes, anodes, solid state electrolytes, and electrolyte additives. With the development of efficient theoretical methods and inexpensive computers, high-throughput theoretical calculations have played an increasingly important role in the discovery of new materials. With the help of automatic simulation flow, many types of materials can be screened, optimized and designed from a structural database according to specific search criteria. In advanced cell technology, new materials for next generation lithium batteries are of great significance to achieve performance, and some representative criteria are: higher energy density, better safety, and faster charge/discharge speed.
Surface structure evolution of cathode materials for Li-ion batteries
Lithium ion batteries are important electrochemical energy storage devices for consumer electronics and the most promising candidates for electrical/hybrid vehicles. The surface chemistry influences the performance of the batteries significantly. In this short review, the evolution of the surface structure of the cathode materials at different states of the pristine, storage and electrochemical reactions are summarized. The main methods for the surface modification are also introduced.
Brief overview of electrochemical potential in lithium ion batteries
The physical fundamentals and influences upon electrode materials' open-circuit voltage (OCV) and the spatial distribution of electrochemical potential in the full cell are briefly reviewed. We hope to illustrate that a better understanding of these scientific problems can help to develop and design high voltage cathodes and interfaces with low Ohmic drop. OCV is one of the main indices to evaluate the performance of lithium ion batteries (LIBs), and the enhancement of OCV shows promise as a way to increase the energy density. Besides, the severe potential drop at the interfaces indicates high resistance there, which is one of the key factors limiting power density.
Lithium-ion transport in inorganic solid state electrolyte
An overview of ion transport in lithium-ion inorganic solid state electrolytes is presented, aimed at exploring and designing better electrolyte materials. Ionic conductivity is one of the most important indices of the performance of inorganic solid state electrolytes. The general definition of solid state electrolytes is presented in terms of their role in a working cell (to convey ions while isolate electrons), and the history of solid electrolyte development is briefly summarized. Ways of using the available theoretical models and experimental methods to characterize lithium-ion transport in solid state electrolytes are systematically introduced. Then the various factors that affect ionic conductivity are itemized, including mainly structural disorder, composite materials and interface effects between a solid electrolyte and an electrode. Finally, strategies for future material systems, for synthesis and characterization methods, and for theory and calculation are proposed, aiming to help accelerate the design and development of new solid electrolytes.
Multi-scale computation methods: Their applications in lithium-ion battery research and development
Based upon advances in theoretical algorithms, modeling and simulations, and computer technologies, the rational design of materials, cells, devices, and packs in the field of lithium-ion batteries is being realized incrementally and will at some point trigger a paradigm revolution by combining calculations and experiments linked by a big shared database, enabling accelerated development of the whole industrial chain. Theory and multi-scale modeling and simulation, as supplements to experimental efforts, can help greatly to close some of the current experimental and technological gaps, as well as predict path-independent properties and help to fundamentally understand path-independent performance in multiple spatial and temporal scales.
Redox-assisted Li+-storage in lithium-ion batteries
Interfacial charge transfer is the key kinetic process dictating the operation of lithium-ion battery. Redox-mediated charge propagations of the electronic (e- and h+) and ionic species (Li+) at the electrode-electrolyte interface have recently gained increasing attention for better exploitation of battery materials. This article briefly summarises the energetic and kinetic aspects of lithium-ion batteries, and reviews the recent progress on various redox-assisted Li+ storage approaches. From molecular wiring to polymer wiring and from redox targeting to redox flow lithium battery, the role of redox mediators and the way of the redox species functioning in lithium-ion batteries are discussed.
Scientific and technological challenges toward application of lithium-sulfur batteries
Recent progress in improving Li-S batteries' cathodes, anodes, and electrolytes via different approaches is summarized. The poor conductivity of sulfur cathodes, the dissolution of polysulfide intermediates, and the high reactivity of metal Li anodes currently motivate a great deal of research. Urgent challenges concerning Li anodes are also emphasized.
All-solid-state lithium batteries with inorganic solid electrolytes: Review of fundamental science
The scientific basis of all-solid-state lithium batteries with inorganic solid electrolytes is reviewed briefly, touching upon solid electrolytes, electrode materials, electrolyte/electrode interface phenomena, fabrication, and evaluation. The challenges and prospects are outlined as well.
Correlation effects on the fine-structure splitting within the 3d9 ground configuration in highly-charged Co-like ions
Accurate spectroscopic constants of the lowest two electronic states in S2 molecule with explicitly correlated method
A computational scheme for accurate spectroscopic constants was presented in this work and applied to the lowest two electronic states of sulfur dimer. A high-level ab initio calculation utilizing explicitly correlated multireference configuration interaction method (MRCI-F12) was performed to compute the potential energy curves (PECs) of the ground triplet X3Σg- and first excited singlet a1Δg states of sulfur dimer with cc-pCVXZ-F12(X=m T, Q) basis sets. The effects of Davidson modification, core-valence correlation correction, and scalar relativistic correction on the spectroscopic constants were examined. The vibration-rotation spectra of the two electronic states were provided. Our computational results show excellent agreement with existing available experimental values, and the errors of main spectroscopic constants are within 0.1% order of magnitude. The present computational scheme is cheap and accurate, which is expected for extensive investigations on the potential energy curves or surfaces of other molecular systems.
Phase equilibrium of Cd1-xZnxS alloys studied by first-principles calculations and Monte Carlo simulations
New developments in the multiscale hybrid energy density computational method
Stark effect of the hyperfine structure of ICl in its rovibronic ground state: Towards further molecular cooling
Numerical analyses on optical limiting performances of chloroindium phthalocyanines with different substituent positions
Triple differential cross sections of magnesium in doubly symmetric geometry
Mobility of large clusters on a semiconductor surface: Kinetic Monte Carlo simulation results
Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds
The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice.
A new understanding of inert gas narcosis
Anesthetics are extremely important in modern surgery to greatly reduce the patient's pain. The understanding of anesthesia at molecular level is the preliminary step for the application of anesthetics in clinic safely and effectively. Inert gases, with low chemical activity, have been found to cause anesthesia for centuries, but the mechanism is unclear yet. In this review, we first summarize the progress of theories about general anesthesia, especially for inert gas narcosis, and then propose a new hypothesis that the aggregated rather than the dispersed inert gas molecules are the key to trigger the narcosis to explain the steep dose-response relationship of anesthesia.
Uncovering the underlying physical mechanisms of biological systems via quantification of landscape and flux
In this review, we explore the physical mechanisms of biological processes such as protein folding and recognition, ligand binding, and systems biology, including cell cycle, stem cell, cancer, evolution, ecology, and neural networks. Our approach is based on the landscape and flux theory for nonequilibrium dynamical systems. This theory provides a unifying principle and foundation for investigating the underlying mechanisms and physical quantification of biological systems.
Self-assembly of block copolymers grafted onto a flat substrate: Recent progress in theory and simulations
Development of mean-field electrical double layer theory
In order to understand the electric interfacial behavior, mean field based electric double layer (EDL) theory has been continuously developed over the past 150 years. In this article, we briefly review the development of the EDL model, from the dimensionless Gouy-Chapman model to the symmetric Bikerman-Freise model, and finally toward size-asymmetric mean field theory models. We provide the general derivations within the framework of Helmholtz free energy of the lattice-gas model, and it can be seen that the above-mentioned models are consistent in the sense that the interconversion among them can be achieved by reducing the basic assumptions.
Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique
We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GBOBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide folding landscapes.
Hierarchical processes in β -sheet peptide self-assembly from the microscopic to the mesoscopic level
Under appropriate physicochemical conditions, short peptide fragments and their synthetic mimics have been shown to form elongated cross-β nanostructures through self-assembly. The self-assembly process and the resultant peptide nanostructures are not only related to neurodegenerative diseases but also provide inspiration for the development of novel bionanomaterials. Both experimental and theoretical studies on peptide self-assembly have shown that the self-assembly process spans multiple time and length scales and is hierarchical. β -sheet self-assembly consists of three sub-processes from the microscopic to the mesoscopic level: β -sheet locking, lateral stacking, and morphological transformation. Detailed atomistic simulation studies have provided insight into the early stages of peptide nanostructure formation and the interplay between different non-covalent interactions at the microscopic level. This review gives a brief introduction of the hierarchical peptide self-assembly process and focuses on the roles of various non-covalent interactions in the sub-processes based on recent simulation, experimental, and theoretical studies.
Computational design of proteins with novel structure and functions
Computational design of proteins is a relatively new field, where scientists search the enormous sequence space for sequences that can fold into desired structure and perform desired functions. With the computational approach, proteins can be designed, for example, as regulators of biological processes, novel enzymes, or as biotherapeutics. These approaches not only provide valuable information for understanding of sequence-structure-function relations in proteins, but also hold promise for applications to protein engineering and biomedical research. In this review, we briefly introduce the rationale for computational protein design, then summarize the recent progress in this field, including de novo protein design, enzyme design, and design of protein-protein interactions. Challenges and future prospects of this field are also discussed.
Flexibility of nucleic acids: From DNA to RNA
Amyloid-β peptide aggregation and the influence of carbon nanoparticles
Improvements in continuum modeling for biomolecular systems
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of the biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.
Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We stay away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while addressing statistical physics modeling approaches along with all-atom molecular dynamics simulation studies. We organize this review around our own modeling and simulation practices on a single subunit T7 RNA polymerase, and summarize commensurate studies on structurally similar DNA polymerases as well. For multi-subunit RNA polymerases that have been actively studied in recent years, we leave systematical reviews of the simulation achievements to latest computational chemistry surveys, while covering only representative studies published very recently, including our own work modeling structure-based elongation kinetic of yeast RNA polymerase II. In the end, we briefly go through physical modeling on elongation pauses and backtracking activities of the multi-subunit RNAPs. We emphasize on the fluctuation and control mechanisms of the polymerase actions, highlight the non-equilibrium nature of the operation system, and try to build some perspectives toward understanding the polymerase impacts from the single molecule level to a genome-wide scale.
Multiscale molecular dynamics simulations of membrane remodeling by Bin/Amphiphysin/Rvs family proteins
In vitro three-dimensional cancer metastasis modeling: Past, present, and future
Recent technical advancements enabled atomic resolution CryoEM
With recent breakthroughs in camera and image processing technologies single-particle electron cryo-microscopy (CryoEM) has suddenly gained the attention of structural biologists as a powerful tool able to solve the atomic structures of biological complexes and assemblies. Compared with x-ray crystallography, CryoEM can be applied to partially flexible structures in solution and without the necessity of crystallization, which is especially important for large complexes and assemblies. This review briefly explains several key bottlenecks for atomic resolution CryoEM, and describes the corresponding solutions for these bottlenecks based on the recent technical advancements. The review also aims to provide an overview about the technical differences between its applications in biology and those in material science.
Cavity linewidth narrowing with dark-state polaritons
Steady-state linear optical properties and Kerr nonlinear optical response of a four-level quantum dot with phonon-assisted transition
Stationary entanglement between two nanomechanical oscillators induced by Coulomb interaction
We propose a scheme for entangling two nanomechanical oscillators by Coulomb interaction in an optomechanical system. We find that the steady-state entanglement of two charged nanomechanical oscillators can be obtained when the coupling between them is stronger than a critical value which relies on the detuning. Remarkably, the degree of entanglement can be controlled by the Coulomb interaction and the frequencies of the two charged oscillators.
Fiber fuse behavior in kW-level continuous-wave double-clad field laser
In this study, original experimental data for fiber fuse in kW-level continuous-wave (CW) high power double-clad fiber (DCF) laser are reported. The propagating velocity of the fuse is 9.68 m/s in a 3.1-kW Yb-doped DCF laser. Three other cases in Yb-doped DCF are also observed. We think that the ignition of fiber fuse is caused by thermal mechanism, and the formation of bullet-shaped tracks is attributed to the optical discharge and temperature gradient. The inducements of initial fuse and formation of bullet-shaped voids are analyzed. This investigation of fiber fuse helps better understand the fiber fuse behavior, in order to avoid the catastrophic destruction caused by fiber fuse in high power fiber laser.
Frequency doubled femtosecond Ti:sapphire laser with an assisted enhancement cavity
We report an enhancement cavity for femtosecond Ti:sapphire laser at the repetition rate of 170 MHz. An enhancement factor of 24 is obtained when the injecting pulses have an average power of 1 W and a pulse duration of 80 fs. By placing a BBO crystal at the focus of the cavity, we obtain a 392-mW intracavity doubled-frequency laser, corresponding to a conversion efficiency of 43%. The output power has a long-term stability with a root mean square (RMS) of 0.036%.
Joint transfer of time and frequency signals and multi-point synchronization via fiber network
A system of jointly transferring time signals with a rate of 1 pulse per second (PPS) and frequency signals of 10 MHz via a dense wavelength division multiplex-based (DWDM) fiber is demonstrated in this paper. The noises of the fiber links are suppressed and compensated for by a controlled fiber delay line. A method of calibrating and characterizing time is described. The 1PPS is synchronized by feed-forward calibrating the fiber delays precisely. The system is experimentally examined via a 110 km spooled fiber in laboratory. The frequency stabilities of the user end with compensation are 1.8× 10-14 at 1 s and 2.0× 10-17 at 104 s average time. The calculated uncertainty of time synchronization is 13.1 ps, whereas the direct measurement of the uncertainty is 12 ps. Next, the frequency and 1PPS are transferred via a metropolitan area optical fiber network from one central site to two remote sites with distances of 14 km and 110 km. The frequency stabilities of 14 km link reach 3.0× 10-14 averaged in 1 s and 1.4× 10-17 in 104 s respectively; and the stabilities of 110 km link are 8.3× 10-14 and 1.7× 10-17, respectively. The accuracies of synchronization are estimated to be 12.3 ps for the 14 km link and 13.1 ps for the 110 km link, respectively.
Tunable femtosecond near-infrared source based on a Yb:LYSO-laser-pumped optical parametric oscillator
We demonstrate a widely tunable near-infrared source from 767 nm to 874 nm generated by the intracavity second harmonic generation (SHG) in an optical parametric oscillator pumped by a Yb:LYSO solid-state laser. The home-made Yb:LYSO oscillator centered at 1035 nm delivers an average power of 2 W and a pulse duration as short as 351 fs. Two MgO doped periodically poled lithium niobates (MgO:PPLN) with grating periods of 28.5-31.5 μ in steps of 0.5 μ and 19.5-21.3 μ in steps of 0.2 μ are used for the OPO and intracavity SHG, respectively. The maximum average output power of 180 mW at 798 nm was obtained and the output pulses have pulse duration of 313 fs at 792 nm if a sech2-pulse shape was assumed. In addition, tunable signal femtosecond pulses from 1428 nm to 1763 nm are also realized with the maximum average power of 355 mW at 1628 nm.
Tunable, continuous-wave single-resonant optical parametric oscillator with output coupling for resonant wave
We present a continuous-wave singly-resonant optical parametric oscillator with 1.5% output coupling of the resonant signal wave, based on an angle-polished MgO-doped periodically poled lithium niobate (MgO:PPLN), pumped by a commercial Nd:YVO4 laser at 1064 nm. The output-coupled optical parametric oscillator delivers a maximum total output power of 4.19 W with 42.8% extraction efficiency, across a tuning range of 1717 nm in the near-and mid-infrared region. This indicates improvements of 1.87 W in output power, 19.1% in extraction efficiency and 213 nm in tuning range extension in comparison with the optical parametric oscillator with no output coupling, while at the expense of increasing the oscillation threshold by a factor of ～ 2. Moreover, it is confirmed that the finite output coupling also contributes to the reduction of the thermal effects in crystal.
Optimization of the idler wavelength tunable cascaded optical parametric oscillator based on chirp-assisted aperiodically poled lithium niobate crystal
We present the numerical results for the optimization of the pump-to-idler conversion efficiencies of nanosecond idler wavelength tunable cascaded optical parametric oscillators (OPO) in different wavelength tuning ranges, where the primary signals from the OPO process are recycled to enhance the pump-to-idler conversion efficiencies via the simultaneous difference frequency generation (DFG) process by monolithic aperiodically poled, magnesium oxide doped lithium niobate (APMgLN) crystals. The APMgLN crystals are designed with different chirp parameters for the DFG process to broaden their thermal acceptance bandwidths to different extents. The idler wavelength tuning of the cascaded OPO is realized by changing the temperature of the designed APMgLN crystal and the cascaded oscillation is achieved in a single pump pass singly resonant linear cavity. The pump-to-idler conversion efficiencies with respect to the pump pulse duration and ratio of OPO coefficient to DFG coefficient are calculated by numerically solving the coupled wave equations. The optimal working conditions of the tunable cascaded OPOs pumped by pulses with energies of 350 μJ and 700 μJ are compared to obtain the general rules of optimization. It is concluded that the optimization becomes the interplay between the ratio of OPO coefficient to DFG coefficient and the pump pulse duration when the idler wavelength tuning range and the pump pulse energy are fixed. Besides, higher pump pulse energy is beneficial for reaching higher optimal pump-to-idler conversion efficiency as long as the APMgLN crystal is optimized according to this pump condition. To the best of our knowledge, this is the first numerical analysis of idler wavelength tunable cascaded OPOs based on chirp-assisted APMgLN crystals.
Numerical simulation of modulation to incident laser by submicron to micron surface contaminants on fused silica
Data point selection for weighted least square fitting of cavity decay time constant
Non-Noether symmetries of Hamiltonian systems withconformable fractional derivatives
Two kinds of generalized gradient representationsfor holonomic mechanical systems
Two kinds of generalized gradient systems are proposed and the characteristics of the two systems are studied. The conditions under which a holonomic mechanical system can be considered as one of the two generalized gradient systems are obtained. The characteristics of the generalized gradient systems can be used to study the stability of the holonomic system. Some examples are given to illustrate the application of the results.
Analytical study of Cattaneo-Christov heat flux model for a boundary layer flow of Oldroyd-B fluid
Three-dimensional multi-relaxation-time lattice Boltzmann front-tracking method for two-phase flow
Predetermined control of turbulent boundary layer with a piezoelectric oscillator
With a piezoelectric (PZT) oscillator, the predetermined controls of the turbulent boundary layer (TBL) are effective in reducing the drag force. The stream-wise velocities in the TBL are accurately measured downstream of the oscillator driven by an adjustable power source. The mean velocity profiles in the inner and outer scales are reported and the skin friction stresses with different voltage parameters are compared. Reduction of integral spatial scales in the inner region below y+ of 30 suggests that the oscillator at work breaks up the near-wall stream-wise vortices responsible for high skin friction. For the TBL at Reθ of 2183, the controls with a frequency of 160 Hz are superior among our experiments and a relative drag reduction rate of 26.83% is exciting. Wavelet analyses provide a reason why the controls with this special frequency perform best.
Optimized calculation of the synergy conditions between electron cyclotron current drive and lower hybrid current drive on EAST
The optimized synergy conditions between electron cyclotron current drive (ECCD) and lower hybrid current drive (LHCD) with normal parameters of the EAST tokamak are studied by using the C3PO/LUKE code based on the understanding of the synergy mechanisms so as to obtain a higher synergistic current and provide theoretical reference for the synergistic effect in the EAST experiment. The dependences of the synergistic effect on the parameters of two waves (lower hybrid wave (LHW) and electron cyclotron wave (ECW)), including the radial position of the power deposition, the power value of the LH and EC waves, and the parallel refractive indices of the LHW (N||) are presented and discussed.
Numerical study of the effect of water content on OH production in a pulsed-dc atmospheric pressure helium-air plasma jet
Effects of q-profiles of a weak magnetic shear on energetic ion excited q=1 mode in tokamak plasmas
Conversion of an atomic to a molecular argon ion and low pressure argon relaxation
FT-Raman spectroscopy study of solvent-in-salt electrolytes
Evolution of structure and physical properties in Al-substituted Ba-hexaferrites
A new family of sp3-hybridized carbon phases
Phonon dispersion on Ag (100) surface: A modified analytic embedded atom method study
Ab initio investigation of photoinduced non-thermal phase transition in β -cristobalite
Vortices in dipolar Bose-Einstein condensates in synthetic magnetic field
Phase transition and critical behavior ofspin-orbital coupled spinel ZnV2O4
We present the temperature-dependent susceptibility and specific heat measurement of spinel ZnV2O4. The structural transition with orbital ordering and the antiferromagnetic transition with spin ordering were observed at 50 K and 37 K, respectively. By analysis of the hysteresis behavior between the specific heat curves obtained in warming and cooling processes, the structural transition was confirmed to be the first-order transition, while the antiferromagnetic transition was found to be of the second-order type. At the structural transition, the latent heat and entropy change were calculated from the excess specific heat, and the derivative of pressure with respect to temperature was obtained using the Clausius-Clapayron equation. At the magnetic transition, the width of the critical fluctuation region was obtained to be about 0.5 K by comparing with Gaussian fluctuations. In the critical region, the critical behavior was analyzed by using renormalization-group theory. The critical amplitude ratio A+ /A-=1.46, which deviates from the 3D Heisenburg model; while the critical exponent α is -0.011, which is close to the 3D XY model. We proposed that these abnormal critical behaviors can be attributed to strong spin-orbital coupling accompanied with the antiferromagnetic transition. Moreover, in the low temperature range (2-5 K), the Fermi energy, the density of states near the Fermi surface, and the low limit of Debye temperature were estimated to be 2.42 eV, 2.48 eV-1, and 240 K, respectively.
Characteristics of Li diffusion on silicene and zigzag nanoribbon
Heterogeneous fragmentation of metallic liquid microsheet with high velocity gradient
Large-scale molecular dynamics simulations are performed to study the fragmentation of metallic liquid sheets with high velocity gradient. Dynamic fragmentation of the system involves the formation of a network of fragments due to the growth and coalescence of holes, decomposition of the network into filaments, and further breakup of the filaments into spherical clusters. The final size distribution of the fragmented clusters in the large volume limit is found to obey a bilinear exponential form, which is resulted from the heterogeneous breakup of quasi-cylindrical filaments. The main factors contributing to fragmentation heterogeneity are introduced, including strain rate inhomogeneity and matter distribution nonuniformity of fragments produced during decomposition of the network structure.
Spin texturing in quantum wires with Rashba and Dresselhaus spin-orbit interactions and in-plane magnetic field
Characterization of vertical Au/β -Ga2O3 single-crystal Schottky photodiodes with MBE-grown high-resistivity epitaxial layer
Manipulating coupling state and magnetism of Mn-doped ZnO nanocrystals by changing the coordination environment of Mn via hydrogen annealing
Mn-doped ZnO nanocrystals are synthesized by a wet chemical route and treated in H2/Ar atmosphere with different H2/Ar ratios. It is found that hydrogen annealing could change the coordination environment of Mn in ZnO lattice and manipulate the magnetic properties of Mn-doped ZnO. Mn ions initially enter into interstitial sites and a Mn3+O6 octahedral coordination is produced in the prepared Mn-doped ZnO sample, in which the nearest neighbor Mn3+ and O2 ions could form a Mn3+-O2--Mn3+ complex. After H2 annealing, interstitial Mn ions can substitute for Zn to generate the Mn2+O4 tetrahedral coordination in the nanocrystals, in which neighboring Mn2+ ions and H atoms could form a Mn2+-O2--Mn2+ complex and Mn-H-Mn bridge structure. The magnetic measurement of the as-prepared sample shows room temperature paramagnetic behavior due to the Mn3+-O2--Mn3+ complex, while the annealed samples exhibit their ferromagnetism, which originates from the Mn-H-Mn bridge structure and the Mn-Mn exchange interaction in the Mn2+-O2--Mn2+ complex.
Modulating doping and interface magnetism ofepitaxial graphene on SiC(0001)
Reverse blocking characteristics and mechanisms in Schottky-drainAlGaN/GaN HEMT with a drain field plate and floating field plates
In-situ SAXS study on PET/ PMMT composites during tensile tests
Unexpected low thermal conductivity and large power factor in Dirac semimetal Cd3As2 Hot!
Thermoelectrics has long been considered as a promising way of power generation for the next decades. So far, extensive efforts have been devoted to the search of ideal thermoelectric materials, which require both high electrical conductivity and low thermal conductivity. Recently, the emerging Dirac semimetal Cd3As2, a three-dimensional analogue of graphene, has been reported to host ultra-high mobility and good electrical conductivity as metals. Here, we report the observation of unexpected low thermal conductivity in Cd3As2, one order of magnitude lower than the conventional metals or semimetals with a similar electrical conductivity, despite the semimetal band structure and high electron mobility. The power factor also reaches a large value of 1.58 mW·m-1·K-2 at room temperature and remains non-saturated up to 400 K. Corroborating with the first-principles calculations, we find that the thermoelectric performance can be well-modulated by the carrier concentration in a wide range. This work demonstrates the Dirac semimetal Cd3As2 as a potential candidate of thermoelectric materials.
Fabrication of superconducting NbN meander nanowires by nano-imprint lithography
Superconducting nanowire single photon detector (SNSPD), as a new type of superconducting single photon detector (SPD), has a broad application prospect in quantum communication and other fields. In order to prepare SNSPD with high performance, it is necessary to fabricate a large area of uniform meander nanowires, which is the core of the SNSPD. In this paper, we demonstrate a process of patterning ultra-thin NbN films into meander-type nanowires by using the nano-imprint technology. In this process, a combination of hot embossing nano-imprint lithography (HE-NIL) and ultraviolet nano-imprint lithography (UV-NIL) is used to transfer the meander nanowire structure from the NIL Si hard mold to the NbN film. We have successfully obtained a NbN nanowire device with uniform line width. The critical temperature (Tc) of the superconducting NbN meander nanowires is about 5 K and the critical current (Ic) is about 3.5 μA at 2.5 K.
Long-distance super-exchange and quantum magnetic relaxation in a hybrid metal-organic framework Hot!
The hybrid metal-organic framework [(CH3)2NH2]Fe(HCOO)3 with a perovskite-like structure exhibits a variety of unusual magnetic behaviors at low temperatures. While the long-distance super-exchange through the Fe-O-CH-O-Fe exchange path leads to a canted antiferromagnetic ordering at TN ～ 19 K, a second transition of magnetic blocking develops at TB ～ 9 K. The stair-shaped magnetization hysteresis loops below TB resemble the behaviors of resonant quantum tunneling of magnetization in single-molecular quantum magnets. Moreover, the magnetic relaxation also exhibits several features of resonant quantum relaxation, such as the exponential law with a single characteristic relaxation time, and the nonmonotonic dependence of relaxation rate on the applied magnetic field with a much faster relaxation around the resonant fields. The origin of quantum tunneling behaviors in the [(CH3)2NH2]Fe(HCOO)3 metal-organic framework is discussed in terms of magnetic phase separation due to the modification of hydrogen bonding on the long-distance super-exchange interaction.
Effect of fluence and ambient environment on the surface and structural modification of femtosecond laser irradiated Ti
Under certain conditions, ultrafast pulsed laser interaction with matter leads to the formation of self-organized conical as well as periodic surface structures (commonly reffered to as, laser induced periodic surface structures, LIPSS). The purpose of the present investigations is to explore the effect of fsec laser fluence and ambient environments (Vacuum & O2) on the formation of LIPSS and conical structures on the Ti surface. The surface morphology was investigated by scanning electron microscope (SEM). The ablation threshold with single and multiple (N=100) shots and the existence of an incubation effect was demonstrated by SEM investigations for both the vacuum and the O2 environment. The phase analysis and chemical composition of the exposed targets were performed by x-ray diffraction (XRD) and energy dispersive x-ray spectroscopy (EDS), respectively. SEM investigations reveal the formation of LIPSS (nano & micro). FFT d-spacing calculations illustrate the dependence of periodicity on the fluence and ambient environment. The periodicity of nano-scale LIPSS is higher in the case of irradiation under vacuum conditions as compared to O2. Furthermore, the O2 environment reduces the ablation threshold. XRD data reveal that for the O2 environment, new phases (oxides of Ti) are formed. EDS analysis exhibits that after irradiation under vacuum conditions, the percentage of impurity element (Al) is reduced. The irradiation in the O2 environment results in 15% atomic diffusion of oxygen.
Superior material qualities and transport properties of InGaN channel heterostructure grown by pulsed metal organicchemical vapor deposition
Pulsed metal organic chemical vapor deposition is introduced into the growth of InGaN channel heterostructure for improving material qualities and transport properties. High-resolution transmission electron microscopy imaging shows the phase separation free InGaN channel with smooth and abrupt interface. A very high two-dimensional electron gas density of approximately 1.85 × 1013 cm-2 is obtained due to the superior carrier confinement. In addition, the Hall mobility reaches 967 cm2/V·s, owing to the suppression of interface roughness scattering. Furthermore, temperature-dependent Hall measurement results show that InGaN channel heterostructure possesses a steady two-dimensional electron gas density over the tested temperature range, and has superior transport properties at elevated temperatures compared with the traditional GaN channel heterostructure. The gratifying results imply that InGaN channel heterostructure grown by pulsed metal organic chemical vapor deposition is a promising candidate for microwave power devices.
Detection and formation mechanism of micro-defects in ultrafine pitch Cu–Cu direct bonding
Improved double-gate armchair silicene nanoribbon field-effect-transistor at large transport bandgap
The electrical characteristics of a double-gate armchair silicene nanoribbon field-effect-transistor (DG ASiNR FET) are thoroughly investigated by using a ballistic quantum transport model based on non-equilibrium Green's function (NEGF) approach self-consistently coupled with a three-dimensional (3D) Poisson equation. We evaluate the influence of variation in uniaxial tensile strain, ribbon temperature and oxide thickness on the on-off current ratio, subthreshold swing, transconductance and the delay time of a 12-nm-length ultranarrow ASiNR FET. A novel two-parameter strain magnitude and temperature-dependent model is presented for designing an optimized device possessing balanced amelioration of all the electrical parameters. We demonstrate that employing HfO2 as the gate insulator can be a favorable choice and simultaneous use of it with proper combination of temperature and strain magnitude can achieve better device performance. Furthermore, a general model power (GMP) is derived which explicitly provides the electron effective mass as a function of the bandgap of a hydrogen passivated ASiNR under strain.
Quantum dynamics of charge transfer on the one-dimensional lattice: Wave packet spreading and recurrence
The wave function temporal evolution on the one-dimensional (1D) lattice is considered in the tight-binding approximation. The lattice consists of N equal sites and one impurity site (donor). The donor differs from other lattice sites by the on-site electron energy E and the intersite coupling C. The moving wave packet is formed from the wave function initially localized on the donor. The exact solution for the wave packet velocity and the shape is derived at different values E and C. The velocity has the maximal possible group velocity v = 2. The wave packet width grows with time ～ t1/3 and its amplitude decreases ～ t-1/3. The wave packet reflects multiply from the lattice ends. Analytical expressions for the wave packet front propagation and recurrence are in good agreement with numeric simulations.
Application of long-range correlation and multi-fractal analysis for the depiction of drought risk