Protein sequences as special heterogeneous sequences are rare in the amino acid sequence space. The specific sequential order of amino acids of a protein is essential to its 3D structure. On the whole, the correlation between sequence and structure of a protein is not so strong. How well would a protein sequence contain its structural information? How does a sequence determine its native structure? Keeping the globular proteins in mind, we discuss several problems from sequence to structure.
Formation and dissociation mechanisms of C–C+base pairs in acidic and alkaline environments are investigated,employing ab initio quantum chemical calculations.Our calculations suggest that,in an acidic environment,a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C–C+base pair;in an alkaline environment,a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers.In addition,the force for detaching a C–C+base pair was found to be inversely proportional to the distance between the two cytosine monomers.These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.
We present a fully quantum solution to the Gibbs paradox (GP) with an illustration based on a gedanken experiment with two particles trapped in an infinite potential well. The well is divided into two cells by a solid wall, which could be removed for mixing the particles. For the initial thermal state with correct two-particle wavefunction according to their quantum statistics, the exact calculations show the entropy changes are the same for boson, fermion and non-identical particles. With the observation that the initial unmixed state of identical particles in the conventional presentations actually is not of a thermal equilibrium, our analysis reveals the quantum origin of the paradox, and confirms Jaynes' observation that entropy increase in Gibbs mixing is only due to the including more observables. To further show up the subtle role of the quantum mechanism in the GP, we study the different finite size effect on the entropy change and show the work performed in the mixing process is different for various types of particles.
A theoretical evaluation of the collective excitation spectra of nucleus at large deformations is possible within the framework of the dinuclear system(DNS) model, which treats the wave function of the fissioning nucleus as a superposition of a mononucleus configuration and two-cluster configurations in a dynamical way, permitting exchange of nucleons between clusters. In this work the method of calculation of the potential energy and the collective spectrum of fissioning nucleus at scission point is presented. Combining the DNS model calculations and the statistical model of fission we calculate the angular distribution of fission fragments for the neutron–induced fission of239 Pu.
The competition between attraction and diffusion determines the kinetics of non-equilibrium aggregation process.The formation of silver nanoclusters through non-equilibrium aggregation of silver atoms in solution was simulated by molecular dynamics as a model system to study the influence of the competition between attraction and diffusion on the aggregation process by varying concentration and temperature.It has been found that the aggregation time decreases monotonically with increasing concentration of silver atoms because of increasing attraction,while initially decreasing and then increasing with increasing temperature because of the competition between accelerated attractive motion and increasing diffusive motion of silver atoms.A mean field approximation was employed to develop a phenomenological model describing the mechanism of temperature dependence of aggregation time.
We provide a general dynamical approach for the quantum Zeno and anti-Zeno efects in an open quantum system under repeated non-demolition measurements.In our approach the repeated measurements are described by a general dynamical model without the wave function collapse postulation.Based on that model,we further study both the short-time and long-time evolutions of the open quantum system under repeated non-demolition measurements,and derive the measurement-modified decay rates of the excited state.In the cases with frequent ideal measurements at zero-temperature,we re-obtain the same decay rate as that from the wave function collapse postulation(Nature,2000,405:546).The correction to the ideal decay rate is also obtained under the non-ideal measurements.Especially,we find that the quantum Zeno and anti-Zeno efects are possibly enhanced by the non-ideal natures of measurements.For the open system under measurements with arbitrary period,we generally derive the rate equation for the long-time evolution for the cases with arbitrary temperature and noise spectrum,and show that in the long-time evolution the noise spectrum is efectively tuned by the repeated measurements.Our approach is also able to describe the quantum Zeno and anti-Zeno efects given by the phase modulation pulses,as well as the relevant quantum control schemes.
In this review, we briefly review recent works on hybrid(nano) opto-mechanical systems that contain both mechanical oscillators and diamond nitrogen-vacancy(NV) centers. We also review two different types of mechanical oscillators. The first one is a clamped mechanical oscillator, such as a cantilever, with a fixed frequency. The second one is an optically trapped nano-diamond with a built-in nitrogen-vacancy center. By coupling mechanical resonators with electron spins, we can use the spins to control the motion of mechanical oscillators. For the first setup, we discuss two different coupling mechanisms, which are magnetic coupling and strain induced coupling. We summarize their applications such as cooling the mechanical oscillator, generating entanglements between NV centers, squeezing spin ensembles etc. For the second setup, we discuss how to generate quantum superposition states with magnetic coupling, and realize matter wave interferometer. We will also review its applications as ultra-sensitive mass spectrometer. Finally, we discuss new coupling mechanisms and applications of the field.
In this paper, we demonstrate experimentally switching a cantilever between its optomechanical bistable states in a low finesse optical cavity. Our experiment shows that the deformation of cantilever can be manipulated by tuning the cavity resonance. When the laser power increases across the threshold value of 110 ?W, optomechanical bistability is induced by strong static photothermal backaction at room temperature. Numerical calculation revealed that the bistable effect originates from the multi-well potential created via the optomechanical interaction. Switching of the cantilever between the bistable states was achieved by tuning the cavity to the corresponding boundaries of the bistable region, where the barrier between the bistable states vanishes.
The role of tensor force on the collision dynamics of16O+16O is investigated in the framework of a fully three-dimensional timedependent Hartree-Fock theory.The calculations are performed with modern Skyrme energy functional plus tensor terms.Particular attention is given on the analysis of dissipation dynamics in heavy-ion collisions.The energy dissipation is found to decrease as an initial bombarding energy increases in deep-inelastic collisions for all the Skyrme parameter sets studied here because of the competition between the collective motion and the single-particle degrees of freedom.We reveal that the tensor forces may either enhance or reduce the energy dissipation depending on the different parameter sets.The fusion cross section without tensor force overestimates the experimental value by about 25%,while the calculation with tensor force T11 has good agreement with experimental cross section.
