Search Results (19 total)

The three-dimensional structure of a protein can be treated as a complex network composed of amino acids, and the network properties can help us to understand the relationship between structure and function. Since the amino acid network of a protein is formed in the process of protein folding, it is difficult for general network models to explain its evolving mechanism. Based on the perspective of protein folding, we propose an evolving model for amino acid networks. In our model, the evolution starts from the amino acid sequence of a native protein and it is guided by two generic assumptions: i.e., the neighbor preferential rule and the energy preferential rule. We find that the neighbor preferential rule predominates the general network properties and the energy preferential rule predominates the specific biological structure characteristics. Applied to native proteins, our model mimics the features of amino acid networks well.

A critical process in high-brightness photoinjectors is emittance compensation, which brings under control the correlated transverse emittance growth due to the linear space-charge force. Although emittance compensation has been used and studied for almost two decades, the exact criteria to achieve emittance compensation is not as clear as it should be. In this paper, a perturbative analysis of slice envelopes and emittance evolution close to any reference envelope is developed, via which space-charge and chromatic effects are investigated. A new criterion for emittance compensation is found, which is complementary to the well-known matching condition for the invariant envelope and agrees very well with simulations.

A method is proposed to construct the weighted amino acid network. The weight of the link is based on the contact energy between residues. For the 197 proteins with low homology, the “small-world” property was studied based on this method. Additionally, analyses were carried out for the statistic characteristics of the network parameters, the influence of the weight on the network parameters, the network parameter difference of amino acids, and the links between the hydrophobic and hydrophilic residues. Using this method, we studied the network parameter change for the protein chymotrypsin inhibitor 2 (CI2) on its high-temperature unfolding pathway. It is found that the unfolding of the protein is mainly exhibited as the derogation of the hydrophobic core and the shortest path length rise in the unfolding process. This work is helpful for studies of protein folding and the relationship between structure and function using complex network theory.

The duration of the x-ray pulse generated at a synchrotron light source is typically tens of picoseconds. Shorter pulses are highly desired by the users. In electron storage rings, the vertical beam size is usually orders of magnitude less than the bunch length due to radiation damping; therefore, a shorter pulse can be obtained by slitting the vertically tilted bunch. Zholents proposed tilting the bunch using rf deflection. We found that tilted bunches can also be generated by a dipole magnet kick. A vertical tilt is developed after the kick in the presence of nonzero chromaticity. The tilt was successfully observed and a 4.2-ps pulse was obtained from a 27-ps electron bunch at the Advanced Photon Source. Based on this principle, we propose a short-pulse generation scheme that produces picosecond x-ray pulses at a repetition rate of 1–2 kHz, which can be used for pump-probe experiments.

We show that the band gap bowing trends observed in III-V alloys containing dilute concentrations of Sb or Bi can be explained within the framework of the valence-band anticrossing model. Hybridization of the extended p-like states comprising the valence band of the host semiconductor with the close-lying localized p-like states of Sb or Bi leads to a nonlinear shift of the valence-band edge and a reduction of the band gap. The two alloys GaSb_xAs_1−x and GaBi_xAs_1−x are explored in detail, and the results are extrapolated to additional systems.

A general Hamiltonian suitable for perturbative analysis of rapidly accelerating beams is derived from first principles. With the proper choice of coordinates, the resulting Hamiltonian has a simple and familiar form, yet is able to take into account the rapid acceleration, rf focusing, magnetic focusing, and average space-charge forces in rf photoinjectors. From the linear Hamiltonian, the beam-envelope evolution is solved and analyzed, which better illuminates the invariant-envelope solution as well as the theory of emittance compensation. The third-order nonlinear Hamiltonian is derived and analyzed to some extent. To make the analysis systematic and self-contained, alternative derivations are given for the smoothed ponderomotive rf focusing and the transfer matrix of a rf cavity.

To have a clear insight into the nanowire formation upon catalyst assistant chemical vapor deposition (CCVD), we performed the general thermodynamic and kinetic approaches on nanoscale to elucidate the nanowire nucleation in CCVD with respect to the capillary effect of the nanosized curvature of nanowire nuclei in the initial growing. For the issue of catalyst nanoparticles on nanowires tip or substrate, we deduced the nucleation thermodynamic criteria and diffusion kinetic criteria on the basis of the proposed thermodynamic and kinetic analyses on nanoscale. Taking Si nanowires as the example, we compared the experimental data with the theoretical predictions, and found that they are consistent. We expected that the thermodynamic and kinetic criteria at the nanometer scale to be a general approach applicable to understand nanowires formation in CCVD.

The thermodynamic nucleation and the phase transition of cubic boron nitride (c-BN) on nanoscale is performed with respect to the effect of nanosize-induced additional pressure on the Gibbs free energy of c-BN critical nuclei and the phase transition probability from hexagonal boron nitride (h-BN) to c-BN in the c-BN nanocrystals formation upon pulsed-laser ablation in liquid. The thermodynamic analysis showed that these c-BN critical nuclei with smaller size of 20–30 nm and lower forming energy of 10⁻¹⁵–10⁻¹⁴ J could form in the pressure-temperature region of 4–5 GPa and 3000–3500 K created by pulsed-laser ablation in liquid, in the boron nitride equilibrium phase diagram. The phase transition probabilities of h-BN to c-BN are in the range of 10⁻⁵–10⁻⁴ in the same pressure-temperature region. These theoretical results are well consistent with experimental data.

Rigorous formulas for nonlinear tune shift and β-function distortion due to perturbations in the focusing forces are presented, which complement the well-known tune-shift formula for quadrupole errors. Using these formulas, the calculation of nonlinear chromaticity given by Takao [Phys. Rev. E 70, 016501 (2004)] can be greatly simplified and extended to higher order. In addition, an expression for the nonlinear chromatic β-function distortion is given.

Model-independent analysis of beam dynamics in circular accelerators reveals spatial-temporal modes due to beam oscillations. Although such modes have been shown to be informative, their usefulness is limited by the lack of quantitative understanding in general. Here we present a simple approach to studying the modes analytically, which results in a quantitative understanding of the modes and an algorithm to extract the physical modes by untangling the mixed singular value decomposition modes. Particularly, we focus on the coupled betatron modes that are of great interest for high-energy colliders. A simple relationship between the coupling modes and the lattice functions is established, which not only provides a quantitative understanding but also lays the foundation for using these modes to measure machine properties and beam motion in phase space.

Phase advance and β function are basic lattice functions characterizing the linear properties of an accelerator lattice. Accurate and efficient measurements of these quantities are important for commissioning and operating a machine. For rings with little coupling, we report a new method to measure these lattice functions based on the model-independent analysis technique, which uses beam histories of excited betatron oscillations measured simultaneously at a large number of beam position monitors. It is simple, fast, accurate, and robust. Measurements done at the storage ring of the Advanced Photon Source are reported. Comparisons among various methods are made.

We describe the status of our effort to realize a first neutrino factory and the progress made in understanding the problems associated with the collection and cooling of muons towards that end. We summarize the physics that can be done with neutrino factories as well as with intense cold beams of muons. The physics potential of muon colliders is reviewed, both as Higgs factories and compact high-energy lepton colliders. The status and time scale of our research and development effort is reviewed as well as the latest designs in cooling channels including the promise of ring coolers in achieving longitudinal and transverse cooling simultaneously. We detail the efforts being made to mount an international cooling experiment to demonstrate the ionization cooling of muons.

We report low-temperature Hall-effect and photoluminescence measurements on samples of GaSb lightly doped with carbon in the range of 10¹⁶– 5×10¹⁷ cm^-3. Temperature, excitation intensity, and impurity concentration dependent photoluminescence (PL) measurements were used to determine a shallow acceptor binding energy for carbon in GaSb of 12.9±1 meV. The carbon acceptor PL transition was determined to be due to a combination of donor-acceptor pair and free-to-bound processes. Temperature-dependent Hall-effect analysis of hole concentration and mobility were performed on nominally undoped and lightly carbon-doped epilayers and on bulk undoped Czochralski-grown GaSb. Experimental hole concentrations of the carbon-doped epilayers were fitted to a two acceptor model that included the deep native acceptor and shallow carbon acceptor levels. Activation energies of 8–11 meV were determined for the lightest carbon-doped samples through least-squares fitting of the experimental hole concentration versus temperature. Carbon-doped epilayers showed significantly higher impurity band conduction at low temperatures than Czochralski-grown GaSb due to the shallower nature of the carbon acceptor levels. Hall mobility data confirmed the presence of impurity band conduction below 10 K, in addition to the usual scattering mechanisms.

A linear theory is developed for ionization cooling of muon beams in periodic channels that can provide cooling of the transverse emittances and also of the longitudinal emittance via emittance exchange. The channels incorporate solenoids and quadrupoles for transverse focusing, dipoles to generate dispersion, wedged absorbers for ionization, and rf cavities for acceleration. The beam evolution near equilibrium is described by coupled first-order differential equations for five generalized emittances with two excitation sources. The results should be useful for understanding the cooling process and for designing cooling channels of future muon colliders and neutrino factories.

We present recursive analysis for beam dynamics of periodic focusing channels based on the Fourier coefficients of the focusing function. Formulas for orbit stability and the envelope function are derived. The results should be useful for numerical calculation and for developing analytical understanding of channels employing extended focusing elements. Applications to muon ionization cooling channels are discussed.

Ionization cooling in solenoidal channels, such as that envisioned for the future muon colliders or neutrino factories, is studied. Assuming that the interaction with the ionization material is weak, the evolution of the transverse emittance and angular momentum can be determined analytically. Simple and practical formulas are derived for a general cooling configuration as well as for periodic channels. The prediction of these formulas agrees well with those obtained from simulation codes. The method developed here should be useful to other areas of beam physics involving solenoidal focusing.

Using a singular value decomposition of a beam line matrix, composed of many beam position measurements for a large number of pulses, together with the measurement of pulse-by-pulse beam properties or machine attributes, the contributions of each variable to the beam centroid motion can be identified with a greatly improved resolution. The eigenvalues above the noise floor determine the number of significant physical variables. This method is applicable to storage rings, linear accelerators, and any system involving a number of sources and a larger number of sensors with unknown correlations. Applications are presented from the Stanford Linear Collider.

A refined method for calculating the fractal dimensions of proteins is introduced in this article. The fractal dimensions of 90 proteins covering four structural classes of proteins are established using this method. The relationship between the fractal dimension and tertiary structure of proteins is analyzed. The mean value of the fractal dimension D₂ for the global structure of proteins is 1.65, which is very close to the theoretical value 5/3 associated with a self-avoiding random walk in three-dimensional Euclidean space.