Accurate treatments of electrostatics for computer simulations of biological systems: A brief survey of developments and existing problems
Modern computer simulations of biological systems often involve an explicit treatment of the complex interactions among a large number of molecules. While it is straightforward to compute the short-ranged Van der Waals interaction in classical molecular dynamics simulations, it has been a long-lasting issue to develop accurate methods for the long-ranged Coulomb interaction. In this short review, we discuss three types of methodologies for the accurate treatment of electrostatics in simulations of explicit molecules: truncation-type methods, Ewald-type methods, and mean-field-type methods. Throughout the discussion, we brief the formulations and developments of these methods, emphasize the intrinsic connections among the three types of methods, and focus on the existing problems which are often associated with the boundary conditions of electrostatics. This brief survey is summarized with a short perspective on future trends along the method developments and applications in the field of biological simulations.
Computational studies on the interactions of nanomaterials with proteins and their impacts
The intensive concern over the biosafety of nanomaterials demands the systematic study of the mechanisms underlying their biological effects. Many of the effects of nanomaterials can be attributed to their interactions with proteins and their impacts on protein function. On the other hand, nanomaterials show potential for a variety of biomedical applications, many of which also involve direct interactions with proteins. In this paper, we review some recent computational studies on this subject, especially those investigating the interactions of carbon and gold nanomaterials. Beside hydrophobic and π-stacking interactions, the mode of interaction of carbon nanomaterials can also be regulated by their functional groups. The coatings of gold nanomaterials similarly adjust their mode of interaction, in addition to coordination interactions with the sulfur groups of cysteine residues and the imidazole groups of histidine residues. Nanomaterials can interact with multiple proteins and their impacts on protein activity are attributed to a wide spectrum of mechanisms. These findings on the mechanisms of nanomaterial-protein interactions can further guide the design and development of nanomaterials to realize their application in disease diagnosis and treatment.
Structural modeling of proteins by integrating small-angle x-ray scattering data
Elucidating the structure of large biomolecules such as multi-domain proteins or protein complexes is challenging due to their high flexibility in solution. Recently, an “integrative structural biology” approach has been proposed, which aims to determine the protein structure and characterize protein flexibility by combining complementary high-and low-resolution experimental data using computer simulations. Small-angle x-ray scattering (SAXS) is an efficient technique that can yield low-resolution structural information, including protein size and shape. Here, we review computational methods that integrate SAXS with other experimental datasets for structural modeling. Finally, we provide a case study of determination of the structure of a protein complex formed between the tandem SH3 domains in c-Cb1-associated protein and the proline-rich loop in human vinculin.
Knowledge-based potentials in bioinformatics: From a physicist's viewpoint
Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis on known native structures of proteins. Many knowledge-based potentials for proteins have been proposed. Contrary to most existing review articles which mainly describe technical details and applications of various potential models, the main foci for the discussion here are ideas and concepts involving the construction of potentials, including the relation between free energy and energy, the additivity of potentials of mean force and some key issues in potential construction. Sequence analysis is briefly viewed from an energetic viewpoint.
A multi-field approach to DNA condensation
DNA condensation is an important process in many fields including life sciences, polymer physics, and applied technology. In the nucleus, DNA is condensed into chromosomes. In polymer physics, DNA is treated as a semi-flexible molecule and a polyelectrolyte. Many agents, including multi-valent cations, surfactants, and neutral poor solvents, can cause DNA condensation, also referred to as coil-globule transition. Moreover, DNA condensation has been used for extraction and gene delivery in applied technology. Many physical theories have been presented to elucidate the mechanism underlying DNA condensation, including the counterion correlation theory, the electrostatic zipper theory, and the hydration force theory. Recently several single-molecule studies have focused on DNA condensation, shedding new light on old concepts. In this document, the multi-field concepts and theories related to DNA condensation are introduced and clarified as well as the advances and considerations of single-molecule DNA condensation experiments are introduced.
Theoretical studies on sRNA-mediated regulation in bacteria
Small RNA(sRNA)-mediated post-transcriptional regulation differs from protein-mediated regulation. Through base-pairing, sRNA can regulate the target mRNA in a catalytic or stoichiometric manner. Some theoretical models were built for comparison of the protein-mediated and sRNA-mediated modes in the steady-state behaviors and noise properties. Many experiments demonstrated that a single sRNA can regulate several mRNAs, which causes crosstalk between the targets. Here, we focus on some models in which two target mRNAs are silenced by the same sRNA to discuss their crosstalk features. Additionally, the sequence-function relationship of sRNA and its role in the kinetic process of base-pairing have been highlighted in model building.
Application of self-consistent field theory to self-assembled bilayer membranes
Bilayer membranes self-assembled from amphiphilic molecules such as lipids, surfactants, and block copolymers are ubiquitous in biological and physiochemical systems. The shape and structure of bilayer membranes depend crucially on their mechanical properties such as surface tension, bending moduli, and line tension. Understanding how the molecular properties of the amphiphiles determine the structure and mechanics of the self-assembled bilayers requires a molecularly detailed theoretical framework. The self-consistent field theory provides such a theoretical framework, which is capable of accurately predicting the mechanical parameters of self-assembled bilayer membranes. In this mini review we summarize the formulation of the self-consistent field theory, as exemplified by a model system composed of flexible amphiphilic chains dissolved in hydrophilic polymeric solvents, and its application to the study of self-assembled bilayer membranes.
Firing dynamics of an autaptic neuron
Autapses are synapses that connect a neuron to itself in the nervous system. Previously, both experimental and theoretical studies have demonstrated that autaptic connections in the nervous system have a significant physiological function. Autapses in nature provide self-delayed feedback, thus introducing an additional timescale to neuronal activities and causing many dynamic behaviors in neurons. Recently, theoretical studies have revealed that an autapse provides a control option for adjusting the response of a neuron: e.g., an autaptic connection can cause the electrical activities of the Hindmarsh-Rose neuron to switch between quiescent, periodic, and chaotic firing patterns; an autapse can enhance or suppress the mode-locking status of a neuron injected with sinusoidal current; and the firing frequency and interspike interval distributions of the response spike train can also be modified by the autapse. In this paper, we review recent studies that showed how an autapse affects the response of a single neuron.
The construction of general basis functions in reweighting ensemble dynamics simulations: Reproduce equilibrium distribution in complex systems from multiple short simulation trajectories
Langevin approach with rescaled noise for stochastic channel dynamics in Hodgkin-Huxley neurons
Saturated sodium chloride solution under an external static electric field: A molecular dynamics study
Colloidally deposited nanoparticle wires for biophysical detection
Label-free surface-enhanced infrared spectro-electro-chemical analysis of the Redox potential shift of cytochrome c complexed with a cardiolipin-containing lipid membrane of varied composition
Computational prediction of over-annotated protein-coding genes in the genome of Agrobacterium tumefaciens strain C58
Catch-bond behavior of DNA condensate under tension
Comparison of ligand migration and binding in heme proteins of the globin family
One-dimensional chain of quantum molecule motors as a mathematical physics model for muscle fibers
Thermal vacuum state corresponding to squeezed chaotic light and its application
Dynamics of super-quantum discord and direct control with weak measurement in open quantum system
Decoherence of genuine multipartite entanglement for local non-Markovian-Lorentzian reservoirs
Quantum speed limits for Bell-diagonal states
A note on local unitary equivalence of isotropic-like states
Fast multi-copy entanglement purification with linear optics
We describe an entanglement purification protocol for a polarization Bell state. Different from the previous protocols, it does not require the controlled-not gate, and only uses linear optical elements to complete the task. This protocol requires multi-copy degraded mixed states, which can make this protocol obtain a high fidelity in one purification step. It can also be extended to purify the multi-photon Greenberger-Horne-Zeilinger (GHZ) state. This protocol may be useful in future long-distance communication.
Free-space measurement-device-independent quantum-key-distribution protocol using decoy states with orbital angular momentum
In this paper, we propose a measurement-device-independent quantum-key-distribution (MDI-QKD) protocol using orbital angular momentum (OAM) in free space links, named the OAM-MDI-QKD protocol. In the proposed protocol, the OAM states of photons, instead of polarization states, are used as the information carriers to avoid the reference frame alignment, the decoy-state is adopted to overcome the security loophole caused by the weak coherent pulse source, and the high efficient OAM-sorter is adopted as the measurement tool for Charlie to obtain the output OAM state. Here, Charlie may be an untrusted third party. The results show that the authorized users, Alice and Bob, could distill a secret key with Charlie's successful measurements, and the key generation performance is slightly better than that of the polarization-based MDI-QKD protocol in the two-dimensional OAM cases. Simultaneously, Alice and Bob can reduce the number of flipping the bits in the secure key distillation. It is indicated that a higher key generation rate performance could be obtained by a high dimensional OAM-MDI-QKD protocol because of the unlimited degree of freedom on OAM states. Moreover, the results show that the key generation rate and the transmission distance will decrease as the growth of the strength of atmospheric turbulence (AT) and the link attenuation. In addition, the decoy states used in the proposed protocol can get a considerable good performance without the need for an ideal source.
Unstable and exact periodic solutions of three-particles time-dependent FPU chains
Composition and temperature dependences of site occupation for Al, Cr, W, and Nb in MoSi2
The composition and temperature dependences of site occupation for Al, Cr, W, and Nb in MoSi2 are investigated by using a thermodynamics model and first principles calculations. A simple parameter measuring the substitution energy difference between Si and Mo sites reflects the nature of site occupancy. At 0 K, these elements prefer Si sites in Mo-rich and Mo sites in Si-rich, and show no site preference in stoichiometric MoSi2. At elevated temperature, the site occupation behaviors show strong dependence on both composition and temperature. Some calculated results have been certified in previous experiments.
Entransy analyses of heat-work conversion systems with inner irreversible thermodynamic cycles
Border effect-based precise measurement of any frequency signal
Multistability of delayed complex-valued recurrent neural networks with discontinuous real-imaginary-type activation functions
In this paper, the multistability issue is discussed for delayed complex-valued recurrent neural networks with discontinuous real-imaginary-type activation functions. Based on a fixed theorem and stability definition, sufficient criteria are established for the existence and stability of multiple equilibria of complex-valued recurrent neural networks. The number of stable equilibria is larger than that of real-valued recurrent neural networks, which can be used to achieve high-capacity associative memories. One numerical example is provided to show the effectiveness and superiority of the presented results.
Influence of a strong magnetic field on the hydrogen molecular ion using B-spline-type basis-sets
As an improvement on our previous work [J. Phys. B: At. Mol. Opt. Phys. 45 085101 (2012)], an accurate method combining the spheroidal coordinates and B-spline basis is applied to study the ground state 1σg and low excited states 1σu, 1πg,u,1δg,u,2σg of the H2+ in magnetic fields ranging from 109 Gs (1 Gs=10-4 T) to 4.414×1013 Gs. Comparing the one-center method used in our previous work, the present method has a higher precision with a shorter computing time. Equilibrium distances of the states of the H2+ in strong magnetic fields were found to be accurate to 3～5 significant digits (s.d.) and the total energies 6～11 s.d., even for some antibonding state, such as 1πg, which is difficult for the one-center method to give reliable results while the field strength is B≥q1013 Gs. For the large disagreement in previous works, such as the equilibrium distances of the 1πg state at B=109 Gs, the present data may be used as a reference. Further, the potential energy curves (PECs) and the electronic probability density distributions (EPDDs) of the bound states 1σg, 1πu, 1δg and antibonding states 1σu, 1πg, 1δu for B=1, 10, 100, 1000 a.u. (atomic unit) are compared, so that the different influences of the magnetic fields on the chemical bonds of the bound states and antibonding states are discussed in detail.
Comment on “Relativistic atomic data for W XLVII” by S. Aggarwal et al. [Chin. Phys. B 24 (2015) 053201]
Fast-electron-impact study on excitations of 4d electron of xenon
Solvation of halogen ions in aqueous solutions at 500 K-600 K under 100 atm
Design of ultra wideband microwave absorber effectual for objects of arbitrary shape
Propagation of an Airy-Gaussian beam in uniaxial crystals
Propagation of rotating elliptical Gaussian beams from right-handed material to left-handed material
Increasing the range accuracy of three-dimensional ghost imaging ladar using optimum slicing number method
Dynamical properties of total intensity fluctuation spectrum in two-mode Nd:YVO4 microchip laser
We investigate the total intensity fluctuation spectrum of the two-longitudinal-mode Nd:YVO4 microchip laser (ML). We find that low-frequency relaxation oscillation (RO) peaks still appear in the total intensity fluctuation spectrum, which is different from a previous research result that the low-frequency RO peaks exist in the spectrum of the individual mode but compensate for each other totally in the total intensity fluctuation spectrum. Taking the spatial hole-burning effect into account, one and two-mode rate equations for Nd:YVO4 ML laser are established and studied. Based on the theoretical model, we find that when the gains and losses for two longitudinal models are different, a low-frequency RO peak will appear in the total intensity fluctuation spectrum, while when they share the same gain and loss, the total spectrum will behave like that of a single mode laser. Theoretical simulation results coincide with experimental results very well.
Yb-doped passively mode-locked fiber laser with Bi2Te3-deposited
Analytical model for thermal lensing and spherical aberration in diode side-pumped Nd:YAG laser rod having Gaussian pump profile
Effects of 946-nm thermal shift and broadening on Nd3+:YAG laser performance
Photoluminescence characteristics of ZnTe bulk crystal and ZnTe epilayer grown on GaAs substrate by MOVPE
Tunable negative-index photonic crystals using colloidal magnetic fluids
Strictly non-blocking 4× 4 silicon electro-optic switch matrix
The first path-independent insertion-loss (PILOSS) strictly non-blocking 4× 4 silicon electro-optic switch matrix is reported. The footprint of this switch matrix is only 4.6 mm × 1.0 mm. Using single-arm modulation, the crosstalk measured in this test is-13 dB～-27 dB. And a maximum crosstalk deterioration of 6dB caused by two-path interference is also found.
Acoustic radiation from the submerged circular cylindrical shell treated with active constrained layer damping
Theoretical analysis of transcranial Hall-effect stimulation based on passive cable model
Application of Arnoldi method to boundary layer instability
The Arnoldi method is applied to boundary layer instability, and a finite difference method is employed to avoid the limit of the finite element method. This modus operandi is verified by three comparison cases, i.e., comparison with linear stability theory (LST) for two-dimensional (2D) disturbance on one-dimensional (1D) basic flow, comparison with LST for three-dimensional (3D) disturbance on 1D basic flow, and comparison with Floquet theory for 3D disturbance on 2D basic flow. Then it is applied to secondary instability analysis on the streaky boundary layer under spanwise-localized free-stream turbulence (FST). Three unstable modes are found, i.e., an inner mode at a high-speed center streak, a sinuous type outer mode at a low-speed center streak, and a sinuous type outer mode at low-speed side streaks. All these modes are much more unstable than Tollmien-Schlichting (TS) waves, implying the dominant contribution of secondary instability in bypass transition. The modes at strong center streak are more unstable than those at weak side streaks, so the center streak is ‘angerous' in secondary instability.
Study of hysteresis behavior in reactive sputtering of cylindrical magnetron plasma
A computational modeling study on the helium atmospheric pressure plasma needle discharge
A two-dimensional model of He/O2 atmospheric pressure plasma needle discharge
Relationship between Voronoi entropy and the viscosity of Zr36Cu64 alloy melt based on molecular dynamics
Krypton ion irradiation-induced amorphization and nano-crystal formation in pyrochlore Lu2Ti2O7 at room temperature Hot!
Polycrystalline pyrochlore Lu2Ti2O7 pellets are irradiated with 600-keV Kr3+ ions up to a fluence of 1.45× 1016 Kr3+/cm2. Irradiation induced structural modifications are examined by using grazing incidence x-ray diffraction (GIXRD) and cross-sectional transmission electron microscopy (TEM). The GIXRD reveals that amorphous fraction increases with the increase of fluences up to 2× 1015 Kr3+/cm2, and the results are explained with a direct-impact model. However, when the irradiation fluence is higher than 2× 1015 Kr3+/cm2, the amorphous fraction reaches a saturation of ～ 80%. Further TEM observations imply that nano-crystal is formed with a diameter of ～ 10 nm within the irradiation layer at a fluence of 4×1015 Kr3+/cm2. No full amorphization is achieved even at the highest fluence of 1.45× 1016 Kr3+/cm2 (～ 36 displacement per atom). The high irradiation resistance of pyrochlore Lu2Ti2O7 at higher fluence is explained on the basis of enhanced radiation tolerance of nano-crystal structure.
Effect of combined platinum and electron on the temperature dependence of forward voltage in fast recovery diode
Electronic structures and magnetisms of the Co2TiSb1-xSnx (x=0, 0.25, 0.5) Heusler alloys: A theoretical study of the shape-memory behavior
Material properties dependent on the thermal transport in a cylindrical nanowire
Effects of temperature gradient on the interface microstructure and diffusion of diffusion couples: Phase-field simulation
Multiple patterns of diblock copolymer confined in irregular geometries with soft surface
Interfacial and electrical characteristics of a HfO2/n-InAlAs MOS-capacitor with different dielectric thicknesses
Electrical properties and microstructural characterization of Ni/Ta contacts to n-type 6H-SiC
Raman phonons in multiferroic FeVO4 crystals
Multiferroic materials are promising candidates for next-generation multi-functional devices, because of the coexistence of multi-orders and the coupling between the orders. FeVO4 has been confirmed to be a multiferroic compound, since it exhibits both ferroelectricity and antiferromagnetic ordering at low temperatures. In this paper, we have performed careful Raman scattering measurements on high-quality FeVO4 single crystals. The compound has a very rich phonon structure due to its low crystal symmetry (P-1) and at least 47 Raman-active phonon modes have been resolved in the low and hightemperature spectra. Most of the observed modes are well assigned with aid of first-principles calculations and symmetry analysis. The present study provides an experimental basis for exploring spin-lattice coupling and the mechanism of multiferroicity in FeVO4
First-principles calculation of the electronic structure, chemical bonding, and thermodynamic properties of β-US2
Spin-valley quantum Hall phases in graphene
Spoof surface plasmons resonance effect and tunable electric response of improved metamaterial in the terahertz regime
Shape effects on the ground-state energy of a three-electronquantum dot
In this work we will theoretically study the ground-state electronic structure of three-electron polygonal quantum dots by means of the configuration interaction method. Transition from a weakly correlated regime to a strongly correlated regime is investigated for quantum dots with hexagonal, square, and triangular geometries. Our numerical results reveal that the ground-state spin and the charge density distribution of the system are sensitive to the shape of the quantum dot.
High-k gate dielectric GaAs MOS device with LaON as interlayer and NH3-plasma surface pretreatment Hot!
High-k gate dielectric HfTiON GaAs metal-oxide-semiconductor (MOS) capacitors with LaON as interfacial passivation layer (IPL) and NH3-or N2-plasma surface pretreatment are fabricated, and their interfacial and electrical properties are investigated and compared with their counterparts that have neither LaON IPL nor surface treatment. It is found that good interface quality and excellent electrical properties can be achieved for a NH3-plasma pretreated GaAs MOS device with a stacked gate dielectric of HfTiON/LaON. These improvements should be ascribed to the fact that the NH3-plasma can provide H atoms and NH radicals that can effectively remove defective Ga/As oxides. In addition, LaON IPL can further block oxygen atoms from being in-diffused, and Ga and As atoms from being out-diffused from the substrate to the high-k dielectric. This greatly suppresses the formation of Ga/As native oxides and gives rise to an excellent high-k/GaAs interface.
Influence of ultra-thin TiN thickness (1.4 nm and 2.4 nm) on positive bias temperature instability (PBTI) of high-k/metal gate nMOSFETs with gate-last process
Investigation of trap states in Al2O3 InAlN/GaN metal-oxide-semiconductor high-electron-mobility transistors
Structures and electrical properties of pure and vacancy-included ZnO NWs of different sizes
Multi-step shot noise spectrum induced by a local large spin
First-principles simulation of Raman spectra and structural properties of quartz up to 5 GPa
Study of Nb/NbxSi1-x/Nb Josephson junction arrays
Observation of spin glass transition in spinel LiCoMnO4
Structure, morphology, and magnetic properties of high-performance NiCuZn ferrite
Fabrication and magnetic properties of 4SC(NH2)2-Ni0.97Cu0.03Cl2 single crystals
Al-doping-induced magnetocapacitance in the multiferroic AgCrS2
In this paper, multiferroics and magnetocapacitive effect of triangular-lattice antiferromagnet AgAl0.02Cr0.98S2 are investigated by magnetic, ferroelectric, pyroelectric current and dielectric measurement. We find that it is a multiferroic material and the magnetocapacitive effect reaches a factor of up to 90 in an external field of 7 T. The results imply the further possibility of synthesizing the magnetocapacitive materials by modifying the frustrated spin structure in terms of a few B-site doping nonmagnetic ions.
Spin frustration and magnetic ordering in triangular lattice antiferromagnet Ca3CoNb2O9 Hot!
We synthesized a quasi-two-dimensional distorted triangular lattice antiferromagnet Ca3CoNb2O9, in which the effective spin of Co2+ is 1/2 at low temperatures, whose magnetic properties were studied by dc susceptibility and magnetization techniques. The x-ray diffraction confirms the quality of our powder samples. The large Weiss constant θCW～-55 K and the low Neel temperature TN～ 1.45 K give a frustration factor f=|θCW/TN|≈ 38, suggesting that Ca3CoNb2O9 resides in strong frustration regime. Slightly below TN, deviation between the susceptibility data under zero-field cooling (ZFC) and field cooling (FC) is observed. A new magnetic state with 1/3 of the saturate magnetization Ms is suggested in the magnetization curve at 0.46 K. Our study indicates that Ca3CoNb2O9 is an interesting material to investigate magnetism in triangular lattice antiferromagnets with weak anisotropy.
Multifold polar states in Zn-doped Sr0.9Ba0.1TiO3 ceramics
We investigate the effect of Zn doping on the dielectricity and ferroelectricity of a series of polycrystalline Sr0.9-xZnxBa0.1TiO3 (0.0% ≤ x ≤ 5.0%) ceramics. It is surprisingly observed that the Zn doping will produce the multifold polar states, i.e., the Zn-doped ceramic will convert a reduced polar state into an enhanced polar state, and eventually into a stabilized polar state with increasing the doping level x. It is revealed that in the background of quantum fluctuations, the competition between the Zn-doping-induced lattice contraction and the Ba-doping-induced lattice expansion is responsible for both the reduced polar state and the enhanced polar state coming into being. Also, the addition of the antiferrodistortive effect, which is the antipolar interaction originating from the opposite tilted-TiO6 octahedra rotation, represents the core physics behind the stabilized polar state.
First-principles study of the relaxor ferroelectricity of Ba(Zr, Ti)O3
Comparative research on the optical properties of three surface patterning ZnO ordered arrays
Ultrahigh frequency tunability of aperture-coupled microstrip antenna via electric-field tunable BST
Variation of efficiency droop with quantum well thickness in InGaN/GaN green light-emitting diode
Optical properties of F-and H-terminated armchair silicon nanoribbons
Dielectric and magnetic properties of (Zn, Co) co-doped SnO2 nanoparticles
Charge trapping in surface accumulation layer of heavily doped junctionless nanowire transistors
Optimal satisfaction degree in energy harvesting cognitive radio networks
Al-doping influence on crystal growth of Ni-Al alloy: Experimental testing of a theoretical model
Recently, a condensing potential model was developed to evaluate the crystallization ability of bulk materials [Ye X X, Ming C, Hu Y C and Ning X J 2009 J. Chem. Phys. 130 164711 and Peng K, Ming C, Ye X X, Zhang W X, Zhuang J and Ning X J 2011 Chem. Phys. Lett. 501 330], showing that the best temperature for single crystal growth is about 0.6 Tm, where Tm is the melting temperature, and for Ni-Al alloy, more than 6 wt% of Al-doping will badly reduce the crystallization ability. In order to verify these predictions, we fabricated Ni-Al films with different concentrations of Al on Si substrates at room temperature by pulsed laser deposition, and post-annealed the films at 833, 933, 1033 (～ 0.6 Tm), 1133, and 1233 K in vacuum furnace, respectively. The x-ray diffraction spectra show that annealing at 0.6 Tm is indeed best for larger crystal grain formation, and the film crystallization ability remarkably declines with more than 6-wt% Al doping.
Energy dependence on the electric activities of a neuron
Linear-fitting-based similarity coefficient map for tissue dissimilarity analysis in T2*-w magnetic resonance imaging
Bayesian-MCMC-based parameter estimation of stealth aircraft RCS models