De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase

Classical swine fever virus (CSFV) non-structural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp), a key enzyme which initiates RNA replication by a de novo mechanism without a primer and is a potential target for anti-virus therapy. We expressed the NS5B protein in Escherichia coli. The rGTP can stimulate de novo initiation of RNA synthesis and mutation of the GDD motif to Gly-Asp-Asp (GAA) abolishes the RNA synthesis. To better understand the mechanism of viral RNA synthesis in CSFV, a three-dimensional model was built by homology modeling based on the alignment with several virus RdRps. The model contains 605 residues folded in the characteristic fingers, palm and thumb domains. The fingers domain contains an N-terminal region that plays an important role in conformational change. We propose that the experimentally observed promotion of polymerase efficiency by rGTP is probably due to the conformational changes of the polymerase caused by binding the rGTP. Mutation of the GDD to GAA interferes with the interaction between the residues at the polymerase active site and metal ions, and thus renders the polymerase inactive. (c) 2005 Elsevier B.V. All rights reserved.

Classical two-site fidelity and quantum phase transitions in the Ising model and the extended Hubbard model

In this Letter, the classical two-site-ground-state fidelity (CTGF) is exploited to identify quantum phase transitions (QPTs) for the transverse field Ising model (TFIM) and the one-dimensional extended Hubbard model (EHM). Our results show that the CTGF exhibits an abrupt change around the regions of criticality and can be used to identify QPTs in spin and fermionic systems. The method is especially convenient when it is connected with the density-matrix renormalization group (DMRG) algorithm. (C) 2008 Elsevier B.V. All rights reserved.

Detecting quantum entanglement by means of local operations and classical communication

Based on the positive maps separability criterion, we present a method for the detection of quantum entanglement of a shared bipartite quantum state, within the "distant labs" paradigm, using only local operations and classical communication.

Noiseless method for checking the Peres separability criterion by local operations and classical communication

We present a method for checking the Peres separability criterion in an arbitrary bipartite quantum state rho(AB) within local operations and classical communication scenario. The method does not require noise operation which is needed in making the partial transposition map physically implementable. The main task for the two observers, Alice and Bob, is to measure some specific functions of the partial transposed matrix. With these functions, they can determine the eigenvalues of rho(T)(AB)(B), among which the minimum serves as an entanglement witness.

Method for measuring two-qubit entanglement of formation by local operations and classical communication

We present a parametrically efficient method for measuring the entanglement of formation E-f in an arbitrarily given unknown two-qubit state rho(AB) by local operations and classical communication. The two observers, Alice and Bob, first perform some local operations on their composite systems separately, by which the desired global quantum states can be prepared. Then they estimate seven functions via two modified local quantum networks supplemented a classical communication. After obtaining these functions, Alice and Bob can determine the concurrence C and the entanglement of formation E-f.

Detecting a set of entanglement measures in an unknown tripartite quantum state by local operations and classical communication

We propose a more general method for detecting a set of entanglement measures, i.e., negativities, in an arbitrary tripartite quantum state by local operations and classical communication. To accomplish the detection task using this method, three observers do not need to perform partial transposition maps by the structural physical approximation; instead, they only need to collectively measure some functions via three local networks supplemented by a classical communication. With these functions, they are able to determine the set of negativities related to the tripartite quantum state.

Method for detecting concurrence without the structural physical approximation by local operations and classical communication

We present a modified method for detecting the concurrence in an arbitrary two-qubit quantum state rho(AB) with local operations and classical communication. In this method, it is not necessary for the two observers to prepare the quantum state rho(AB) by the structural physical approximation. Their main task is to measure four specific functions via two local quantum networks. With these functions they can determine the concurrence and then the entanglement of formation.

Coherent classical-path description of deep tunneling

A central challenge to the semiclassical description of quantum mechanics is the quantum phenomenon of "deep" tunneling. Here we show that real time classical trajectories suffice to account correctly even for deep quantum tunneling, using a recently formulated semiclassical initial value representation series of the quantum propagator and a prefactor free semiclassical propagator. Deep quantum tunneling is effected through what we term as coherent classical paths which are composed of one or more classical trajectories that lead from reactant to product but are discontinuous along the way. The end and initial phase space points of consecutive classical trajectories contributing to the coherent path are close to each other in the sense that the distance between them is weighted by a coherent state overlap matrix element. Results are presented for thermal and energy dependent tunneling through a symmetric Eckart barrier.

Investigation of "Rearrangement Step" in classical Beckmann rearrangement mechanism over solid acid by means of O-18 isotopic

The reaction mechanism of the Beckmann rearrangement over B2O3/gamma-Al2O3 and TS-1 in the gas phase has been investigated by isotope labeling approach. The isotopic labeled products were measured by mass spectrometry method. By exchanging oxygen with H, 180 in the rearrangement step, it was found that the exchange reaction between cyclohexanone oxime and (H2O)-O-18 over B2O3/-gamma-Al2O3 and TS-1 could only be carried out in some extent. It suggested that the dissociation of nitrilium, over solid acids be not completely free as the classical mechanism. A concept of the dissociation degree (alpha) that is defined as the ratio of the dissociated intermediate nitrilium to the total intermediate nitrilium has been proposed. By fitting the experimental values with the calculation equation of isotopic labeled products, it is obtained that a values for B2O3/-gamma-Al2O3 and TS-1 are 0.199 and 0.806 at the reaction conditions, respectively.

Qualitative and Quantitative Knowledge in Classical Mechanics

This thesis investigates what knowledge is necessary to solve mechanics problems. A program NEWTON is described which understands and solves problems in mechanics mini-world of objects moving on surfaces. Facts and equations such as those given in mechanics text need to be represented. However, this is far from sufficient to solve problems. Human problem solvers rely on "common sense" and "qualitative" knowledge which the physics text tacitly assumes to be present. A mechanics problem solver must embody such knowledge. Quantitative knowledge given by equations and more qualitative common sense knowledge are the major research points exposited in this thesis. The major issue in solving problems is planning. Planning involves tentatively outlining a possible path to the solution without actually solving the problem. Such a plan needs to be constructed and debugged in the process of solving the problem. Envisionment, or qualitative simulation of the event, plays a central role in this planning process.