A new approach for protein design based on the relative entropy

A new effective and fast minimization approach completely based on the physical theory is proposed for protein design. The sequence space is essentially searched according to the Boltzmann distribution. In this approach, the relative entropy is used as a minimization object function. The method has been tested on an off-lattice model of proteins and the results are better than those obtained from other similar work. Therefore, it can be applied as a uniform frame for both folding and inverse folding of proteins.     

Free energy and the relative entropy

Under the assumption of an identity determining the free energy of a state of a statistical mechanical system relative to a given equilibrium state by means of the relative entropy, it is shown: first, that there is in any physically definable convex set of states a unique state of minimum free energy measured relative to a given equilibrium state; second, that if a state has finite free energy relative to an equilibrium state, then the set of its time translates is a weakly relatively compact set; and third, that a unique perturbed equilibrium state exists following a change in Hamiltonian that is bounded below.     

基于符号相对熵的心电信号时间不可逆性分析

心电图(ECG)信号的时间不可逆性能够反映出心脏的生理功能和健康状态.从短时ECG信号中探测时间不可逆性特征具有重要的现实意义. 文章提出符号相对熵方法(先进行符号化处理,再分别计算它们的时间不可逆性),研究了从MIT-BIH标准数据库中提取的正常窦性心律(normal sinus rhythm,NSR)、心室纤颤(ventricular fibrillation,VF)、心脏猝死(sudden cardiac death,SCD)三种信号.结果表明,这三种信号的时间不可逆性有所不同:NSR信号的时间不可 关键词： 心电信号 相对熵 时间不可逆性     

改进的相对转移熵的癫痫脑电分析

脑电信号是由脑神经活动产生并且始终存在于中枢神经系统的自发性电位活动,是一种重要的生物电信号. 脑电信号是非常微弱的且是非线性的,脑电信号也具有时间不可逆性. 本文提出了一种新的基于正向序列转移概率与逆向序列转移概率的相对熵方法即相对转移熵方法,并应用此方法研究了正常脑电与癫痫脑电的不可逆性,实验结果显示癫痫患者的脑电信号的不可逆性明显小于正常人的脑电信号的不可逆性. 这说明改进的相对转移熵可以作为一个物理过程不可逆程度的度量参数,这使得应用脑电信号区分病人是否患有癫痫疾病具有积极指导意义. 关键词： 相对转移熵 脑电信号 符号化 时间不可逆性     

基于改进的符号相对熵的脑电信号时间不可逆性研究

提出了一种新的使用过程的前向概率和后向概率计算符号相对熵, 并利用符号相对熵来估计熵产的方法. 该方法是基于熵增和过程不可逆特性关系的, 同时证明脑电信号具有时间不可逆特性, 而且该不可逆特性可以提供脑电信号的熵增信息. 最后应用该方法对青老年脑电信号进行数值计算及对比, 结果是老年人的平均能量损耗显著高于年轻人, 证明符号相对熵可以作为一个物理过程不可逆程度的度量参数, 这对脑电信号是否处于积极或平衡状态的诊断治疗具有积极的作用.     

Applicability of the minimum entropy generation method for optimizing thermodynamic cycles

Entropy generation is often used as a figure of merit in thermodynamic cycle optimizations. In this paper, it is shown that the applicability of the minimum entropy generation method to optimizing output power is conditional. The minimum entropy generation rate and the minimum entropy generation number do not correspond to the maximum output power when the total heat into the system of interest is not prescribed. For the cycles whose working medium is heated or cooled by streams with prescribed inlet temperatures and prescribed heat capacity flow rates, it is theoretically proved that both the minimum entropy generation rate and the minimum entropy generation number correspond to the maximum output power when the virtual entropy generation induced by dumping the used streams into the environment is considered. However, the minimum principle of entropy generation is not tenable in the case that the virtual entropy generation is not included, because the total heat into the system of interest is not fixed. An irreversible Carnot cycle and an irreversible Brayton cycle are analysed. The minimum entropy generation rate and the minimum entropy generation number do not correspond to the maximum output power if the heat into the system of interest is not prescribed.     

获得蛋白质激光脉冲升温光源方法的比较研究

触发蛋白质开折叠可以使用激光脉冲升温溶剂产生温跳的方法。红外光谱研究中常用的激光波长为1.9μm,可以通过钬激光器、半导体激光器和光参量振荡(OPO)等非线性光学的方法来实现频率转换。在拥有Nd∶YAG激光光源的情况下,对由LiNbO3晶体差频、临界相位匹配(CPM)的KTP OPO和高压氢气受激拉曼散射所获得的1.9μm激光输出的实验方法进行了比较。结果表明,受激拉曼散射是获得频率转换最有效而便捷的方法。     

The principle of the maximum entropy method

Abstract

The theoretical background of the maximum entropy method (MEM) when it is applied to restore the electron or nuclear densities from diffraction data is described. In MEM, the concept of “entropy” is introduced to deal with any incompleteness in an observation in a proper way. An incompleteness causes some ambiguities in the results to some extent. The essence of the method is to find a solution which necessarily agrees with the observation, leaving the measure of ambiguities (entropy) maximum. A few results for simple structures with typical types of chemical bonding are also presented.     

朗之万方程及其在蛋白质折叠动力学中的应用

研究了朗之万方程的动力学性质,并用它模拟了蛋白质分子的折叠过程.首先在相空间中对朗之万方程做连续映射,发现做布朗运动的粒子在位置坐标上存在明显的概率分布,这表明蛋白质折叠过程中分子空间构型是非遍历的.此外,本文还通过数值模拟得到了去折叠态蛋白质的紧密度指标,并验证了它与实验结果以及其他理论方法的一致性.本文还提出了一种利用重整化方法研究熔球体状态蛋白质的理论模型,并提供了考虑疏水基影响的蛋白质折叠过程的模拟思路. 关键词： 朗之万方程 蛋白质折叠非遍历性 紧密度指标 重整化     

Extraction of spectral functions from Dyson-Schwinger studies via the maximum entropy method

It is shown how to apply the Maximum Entropy Method (MEM) to numerical Dyson-Schwinger studies for the extraction of spectral functions of correlators from their corresponding Euclidean propagators. Differences to the application in lattice QCD are emphasized and, as an example, the spectral functions of massless quarks in cold and dense matter are presented.     

Perturbation theory of von Neumann entropy

In quantum information theory, von Neumann entropy plays an important role; it is related to quantum channel capacities. Only for a few states can one obtain their entropies. In a continuous variable system, numeric evaluation of entropy is not easy due to infinite dimensions. We develop the perturbation theory for systematically calculating von Neumann entropy of a non-degenerate system as well as a degenerate system.     

Topology of protein folding

It is shown that the topological concepts developed previously for the analysis of conformations for strips, double-stranded DNA helices, or elastic thin rods can fruitfully be applied to the study of tertiary folding for complicated protein structures. The topological characteristics determine the integral chirality of proteins and play an important role in the mechanisms of folding and molecular recognition.     

Quantum uncertainty relations of Tsallis relative α entropy coherence based on MUBs

In this paper,we discuss quantum uncertainty relations of Tsallis relative α entropy coherence for a single qubit system based on three mutually unbiased bases.For α∈[1/2,1)U(1,2],the upper and lower bounds of sums of coherence are obtained.However,the above results cannot be verified directly for any α∈(0,1/2).Hence,we only consider the special case of α=1/n+1,where n is a positive integer,and we obtain the upper and lower bounds.By comparing the upper and lower bounds,we find that the upper bound is equal to the lower bound for the special α=1/2,and the differences between the upper and the lower bounds will increase as α increases.Furthermore,we discuss the tendency of the sum of coherence,and find that it has the same tendency with respect to the different θ or φ,which is opposite to the uncertainty relations based on the Rényi entropy and Tsallis entropy.     

Time-dependent radiative transfer using Chapman-Enskog maximum entropy method

The time-dependent problems of radiative transfer involve a coupling between radiation and material energy fields and are nonlinear because of proposed temperature dependence of the medium characteristics in semi-infinite medium with Rayleigh anisotropic scattering. By means of the limited flux, Chapman-Enskog and maximum entropy technique the time-dependent radiative transfer equation has been solved explicitly. The maximum entropy method is used to solve the resulting differential equation for radiative energy density. The calculations are carried out for temperature (normalized dimensionless) Θ(x,τ), radiative energy density and net flux with Rayleigh and anisotropic scattering for different space at different times.     

基于近似熵的突变检测新方法

近似熵是一个有效的非线性动力学指数,能够用于表征时间序列的复杂性,通过滑动窗口技术,近似熵对于一维时间序列的动力学结构突变具有一定的识别能力,但其突变检测结果依赖于子序列长度的选择,且不能准确定位突变点.鉴于此,本文提出了一种新的突变检测方法——滑动移除近似熵.测试结果表明,滑动移除近似熵具有检测结果稳定性好、准确性高等特点,明显优于滑动近似熵和Mann-Kendall方法,其在实际观测资料中的应用进一步证实了新方法的可靠性. 关键词： 近似熵 滑动移除近似熵 突变检测     

Research on the chaos recognition method based on differential entropy

Phase space reconstruction is the first step to recognizing the chaos from observed time series. On the basis of differential entropy, this paper introduces an efficient method to estimate the embedding dimension and the time delay simultaneously. The differential entropy is used to characterize the disorder degree of the reconstructed attractor. The minimum value of the differential entropy corresponds to the optimum set of the reconstructed parameters. Simulated experiments show that the original phase space can be effectively reconstructed from time series, and the accuracy of the invariants in phase space reconstruction is greatly improved. It provides a new method for the identification of chaotic signals from time series.     

The criteria for selecting a method for unfolding neutron spectra based on the information entropy theory

To further expand the application of an artificial neural network in the field of neutron spectrometry, the criteria for choosing between an artificial neural network and the maximum entropy method for the purpose of unfolding neutron spectra was presented. The counts of the Bonner spheres for IAEA neutron spectra were used as a database, and the artificial neural network and the maximum entropy method were used to unfold neutron spectra; the mean squares of the spectra were defined as the differences between the desired and unfolded spectra. After the information entropy of each spectrum was calculated using information entropy theory, the relationship between the mean squares of the spectra and the information entropy was acquired. Useful information from the information entropy guided the selection of unfolding methods. Due to the importance of the information entropy, the method for predicting the information entropy using the Bonner spheres' counts was established. The criteria based on the information entropy theory can be used to choose between the artificial neural network and the maximum entropy method unfolding methods. The application of an artificial neural network to unfold neutron spectra was expanded.     

Relative entropy of entanglement of two-qubit ’X’ states

Two closest single-qubit states could be diagonalised by the same unitary matrix,which helps to find the relative entropy of entanglement of a two-qubit ’X’ state.We formulate two binary equations for the relative entropy of entanglement and the corresponding closest separable state of a given two-qubit ’X’ state.This approach can be applied to get the relative entropy of entanglement of many widely-discussed two-qubit states,such as pure states,Werner states,and so on.     

基于自适应模板法的脑电信号转移熵分析

脑电信号是一种产生机理相当复杂且非常微弱的随机信号, 综合反映了大脑组织的脑电活动及大脑的功能状态. 由于脑电信号的微弱性, 传统的基本模板方法在脑电信号分析上得到了良好的应用. 为进一步提升分析脑电信号的性能, 提出了一种新的基于自适应模板的转移熵方法并分析了青少年脑电与成年人脑电信号. 结果表明: 对于青少年脑电还是成年人脑电, 与基本模板法相比, 基于自适应模板法的转移熵可以更显著地表示脑电信号的耦合作用, 并且具有更好的区分度, 这将能更好地捕捉到信号中的动态信息、系统动力学复杂性的改变. 同时, 该方法将更有利于医学临床诊断的辅助检测, 对脑电信号是否处于病理状态的诊断提供了新的更好的判断依据.