Uncovering the underlying physical mechanisms of biological systems via quantification of landscape and flux

In this review, we explore the physical mechanisms of biological processes such as protein folding and recognition,ligand binding, and systems biology, including cell cycle, stem cell, cancer, evolution, ecology, and neural networks. Our approach is based on the landscape and flux theory for nonequilibrium dynamical systems. This theory provides a unifying principle and foundation for investigating the underlying mechanisms and physical quantification of biological systems.     

Dynamical properties of chemical systems near Hopf bifurcation points

In this paper, we numerically investigate local properties of dynamical systems close to a Hopf bifurcation instability. We focus on chemical systems and present an approach based on the theory of normal forms for determining numerical estimates of the limit cycle that branches off at the Hopf bifurcation point. For several numerically ill-conditioned examples taken from chemical kinetics, we compare our results with those obtained by using traditional approaches where an approximation of the limit cycle is restricted to the center subspace spanned by critical eigenvectors, and show that inclusion of higher-order terms in the normal form expansion of the limit cycle provides a significant improvement of the limit cycle estimates. This result also provides an accurate initial estimate for subsequent numerical continuation of the limit cycle. (c) 2000 American Institute of Physics.     

基于DNA损伤的蛋白调控网络研究

细胞生长的每个阶段都离不开蛋白质相互作用.研究细胞周期的功能、调控机理及参与调控的蛋白质之间的关系对生物工程等领域有重大的应用价值.本文通过研究电离辐射下生物体细胞的DNA损伤后,细胞内以p53为核心的扩展蛋白调控网络的功能、原理及其自修复机理,在现有蛋白网络基础上引入更多蛋白网络调控因子来建立蛋白调控网络,仿真模拟更为全面的细胞周期进程;并且从复杂网络图论和细胞周期调控两个方面分析扩展PMP调控网络的抗扰能力及自修复机理,结果表明:1)蛋白网络在对抗环境中出现的小扰动时具有较强的稳定性.但在面对蓄意攻击时网络的稳定性较差.2)受损的DNA能否被修复取决于p53蛋白的动力学行为,即低损伤与中损伤情况下,p53可诱导细胞周期进程阻滞来完成细胞的自修复;而当高损伤或过损伤时,p53蛋白浓度表现为周期振荡行为并诱导细胞凋亡.     

人体中的伯努利方程

本文从设计实验入手,形象诠释伯努利原理,并从物理学角度出发,根据人体体液流动的实际情况,运用伯努利原理及经典的伯努利方程,从人体血液循环、房水循环的压力形成和改变方面,把物理学的基本理论运用于分析人体体液压力的变化。     

A fractal comparison of real and Austrian business cycle models

Rescaled range and power spectral density analysis are applied to examine a diverse set of macromonetary data for fractal character and stochastic dependence. Fractal statistics are used to evaluate two competing models of the business cycle, Austrian business cycle theory and real business cycle theory. Strong evidence is found for antipersistent stochastic dependence in transactions money (M1) and components of the monetary aggregates most directly concerned with transactions, which suggests an activist monetary policy. Savings assets exhibit persistent long memory, as do those monetary aggregates which include savings assets, such as savings money (M2), M2 minus small time deposits, and money of zero maturity (MZM). Virtually all measures of economic activity display antipersistence, and this finding is invariant to whether the measures are adjusted for inflation, including real gross domestic product, real consumption expenditures, real fixed private investment, and labor productivity. This strongly disconfirms real business cycle theory.     

Probing protein-protein interactions by dynamic force correlation spectroscopy

We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex (P(1)P(2)). The joint distribution P(tau(1),tau(2)) of unbinding lifetimes tau(1) and tau(2), measurable in a compression-tension cycle, which accounts for the internal relaxation dynamics of the proteins under tension, shows that the histogram of tau(1) is not Poissonian. The theory is applied to the forced unbinding of protein P1, modeled as a wormlike chain, from P(1)P(2). We propose a new class of experiments which can resolve the effect of internal protein dynamics on the unbinding lifetimes.     

Quantum measurement II

Some of the basic results of the quantum theory of measurement are reviewed and an application of the theory of sequential measurements to a determination of a geometric phase in a measurement cycle is discussed.     

(火积)理论在热功转换过程中的应用探讨

分析和讨论了(火积)理论在热功转换过程的应用及其局限性.对Carnot循环的分析表明,Carnot循环中系统的(火积)是平衡的,但(火积)和熵之间不存在dG=T2dS这样的联系.对于一般热力学过程,分析表明,在热量传递到内可逆循环中间接对外做功时,现有的(火积)理论可用于系统的分析.讨论了热功转换过程分析中(火积)理论与熵理论的不同.分析表明,两个理论的分析角度及优化输出功的前提条件是不同的.熵产从可用能损失的角度分析热功转换过程,而(火积)理论则从热量势能消耗的角度.当输入系统的可用能给定或者输入系统的热量及热量进、出系统的热力学力给定时,熵产最小化对应于输出功最大;对于(火积)理论,则当输入系统的热量及热量进、出系统的温度给定时,最大(火积)损失对应于最大输出功.同时,它们各自均有局限性.当相应的前提条件不满足时,最大(火积)损失或最小熵产可能不与最大输出功相对应.     

Secondary cycle of equilibria in a system with cosymmetry,its creation by bifurcation and impossibility of symmetric treatment of it

A study is reported of the bifurcation of a cycle of equilibria of an autonomous differential equation with cosymmetry in Hilbert space, which is a simulation of the problem of planar filtrational convection of a fluid in a porous medium. The Lyapunov-Schmidt method and perturbation theory are used to find its amplitude and the damping rate of the dominant mode. It is shown that, in the abstract general model, and also in the problem of convection in a rectangular container, this damping rate varies along the cycle of equilibria. Hence, the cycle of equilibria cannot be an orbit of the action of any symmetry group of the given system. (c) 1995 American Institute of Physics.     

以范德瓦耳斯气体为工质的3种热机循环效率

利用热力学的普遍理论推导了范德瓦尔斯气体热力学函数的表达式,再求出绝热过程和3种等值过程中功和热量的表达式.在此基础上,研究了斯特林循环、奥拓循环和狄塞尔循环的功和效率,并计算和分析了3种循环效率随各种参量变化的关系.     

Performance Analysis and Four-Objective Optimization of an Irreversible Rectangular Cycle

Based on the established model of the irreversible rectangular cycle in the previous literature, in this paper, finite time thermodynamics theory is applied to analyze the performance characteristics of an irreversible rectangular cycle by firstly taking power density and effective power as the objective functions. Then, four performance indicators of the cycle, that is, the thermal efficiency, dimensionless power output, dimensionless effective power, and dimensionless power density, are optimized with the cycle expansion ratio as the optimization variable by applying the nondominated sorting genetic algorithm II (NSGA-II) and considering four-objective, three-objective, and two-objective optimization combinations. Finally, optimal results are selected through three decision-making methods. The results show that although the efficiency of the irreversible rectangular cycle under the maximum power density point is less than that at the maximum power output point, the cycle under the maximum power density point can acquire a smaller size parameter. The efficiency at the maximum effective power point is always larger than that at the maximum power output point. When multi-objective optimization is performed on dimensionless power output, dimensionless effective power, and dimensionless power density, the deviation index obtained from the technique for order preference by similarity to an ideal solution (TOPSIS) decision-making method is the smallest value, which means the result is the best.     

组合脉冲宽带激发2H-平均哈密顿理论计算研究

四级核回波实验通常需要射频脉冲能够激发谱宽超过100 kHz 的信号．在最近的研究中,作者发现组合脉冲COM-II (9018090135 45) 能够在氘核的四级核回波实验中实现宽带激发．此外,作者还结合了八步相位循环的方法,有效消除了由有限脉宽效应造成的谱图扭曲现象．利用了平均哈密顿原理,对该方法进行了理论计算研究．作者采用了自旋为1 的矩阵算符,通过计算解释了八步相位循环能够消除谱图扭曲的原因．     

Optimal spin-entangled electron-hole pair pump

A nonperturbative theory is presented for the creation by an oscillating potential of spin-entangled electron-hole pairs in the Fermi sea. In the weak potential limit, considered earlier by Samuelsson and Büttiker, the entanglement production is much less than 1 bit per cycle. We demonstrate that a strong potential oscillation can produce an average of one Bell pair per two cycles, making it an efficient source of entangled flying qubits.     

超声速气流中的爆震推进理论与研究进展

爆震燃烧近似为等容燃烧,理论上其热循环效率高于基于等压燃烧的爆燃燃烧,在超声速推进系统中具有潜在的应用价值.通过总结超声速气流中的爆震推进理论与研究进展,分析其需要解决的关键科学与技术问题,指导未来高超声速发动机的基础研究.文章重点总结了适用于高超声速飞行的斜爆震发动机、超声速脉冲爆震冲压发动机的基础研究进展.其中对斜爆震发动机的应用模式、相关实验研究思路及方法、数值仿真现状进行了总结分析.对超声速脉冲爆震冲压发动机的基础理论研究现状和目前研究的难点进行了梳理.基于爆震燃烧的超燃冲压发动机具有推进系统自增压、燃烧效率高、推力性能好、推进效率高、燃烧室长度短、结构重量轻等优势,文章总结了该发动机当前的发展进程和最新的研究进展,并对其未来的发展方向以及存在的技术问题进行了分析.      

Cl-ClO催化循环圈的从头算研究

采用分子轨道从头算方法,在B3LYP/6-311 G(3df)和G2水平上研究了极地平流层臭氧损耗的一个基本过程.计算结果明显支持Cl-ClO催化循环圈机理,并且从能量角度解释了了臭氧破坏的基本原因.还对循环圈中各个反应的反应能,生成焓,相对吉布斯自由能做了计算,计算结果相互协调都说明了Cl-ClO催化循环圈破坏臭氧机理的正确性.     

Statistical Thermodynamic Properties of Linear Protein Solutions

利用统计力学理论结合格点模型,讨论了链状蛋白质分子溶液的热力学性质. 结果表明,对于稀溶液来说,溶液的吉布斯函数随蛋白质浓度的增加而降低,蛋白质分子化学势随其浓度增加而升高. 还分析了蛋白质分子链长及温度对溶液吉布斯函数和蛋白质分子化学势的影响. 并且计算讨论了几种第一类抗冻蛋白的化学势.     

More on the infrared renormalization group limit cycle in QCD

We present a detailed study of the recently conjectured infrared renormalization group limit cycle in QCD using chiral effective field theory. It was conjectured that small increases in the up and down quark masses can move QCD to the critical trajectory for an infrared limit cycle in the three-nucleon system. At the critical quark masses, the binding energies of the deuteron and its spin-singlet partner are tuned to zero and the triton has infinitely many excited states with an accumulation point at the three-nucleon threshold. We exemplify three parameter sets where this effect occurs at next-to-leading order in the chiral counting. For one of them, we study the structure of the three-nucleon system in detail using both chiral and contact effective field theories. Furthermore, we investigate the matching of the chiral and contact theories in the critical region and calculate the influence of the limit cycle on three-nucleon scattering observables. PACS 12.38.Aw, 21.45.+v, 11.10.Hi     

Nonequilibrium free energy and information flow of a double quantum-dot system with Coulomb coupling

We build a double quantum-dot system with Coulomb coupling and aim at studying connections among the entropy production, free energy, and information flow. By utilizing concepts in stochastic thermodynamics and graph theory analysis, Clausius and nonequilibrium free energy inequalities are built to interpret local second law of thermodynamics for subsystems. A fundamental set of cycle fluxes and affinities is identified to decompose two inequalities by using Schnakenberg's network theory. Results show that the thermodynamic irreversibility has energy-related and information-related contributions. A global cycle associated with the feedback-induced information flow would pump electrons against the bias voltage, which implements a Maxwell demon.     

IR reflection-absorption spectroscopy of CO adsorbed on palladium

Kinetic theory is used to compute the flux and relative translational kinetic energy incident upon a surface oscillating in a rarefied gas. The flux incident upon the oscillatory surface is deficient in low-velocity molecules from the gas during the reentry half of a vibration cycle, in which the surface moves into the gas, because all molecules which are to strike the oscillatory surface from the gas must cross the plane of maximum surface extension during that cycle. The deficiency is largely compensated for by recapture, during the reentry half of a cycle, of low-velocity molecules emitted during the recession half of the cycle. The result of these two opposing effects is that the average energy of gas-surface collisions, and therefore the temperature rise of an oscillatory surface is greater than that of a constant speed plate of the same rms velocity in the same gas. For argon at 300 K and 10^?3 torr incident upon a surface with an rms velocity of 3.3 × 10³ cm sec^?1 the apparent average temperature of incident molecules is 302.91 ° for an oscillatory surface and 302.63 ° for a constant speed plate. Measurements of the temperature rise of an oscillatory surface offer a way to measure thermal accomodation coefficients.     

Quantum mechanical free energy barrier for an enzymatic reaction

We discuss problems related to in silico studies of enzymes and show that accurate and converged free energy changes for complex chemical reactions can be computed if a method based on a thermodynamic cycle is employed. The method combines the sampling speed of molecular mechanics with the accuracy of a high-level quantum mechanics method. We use the method to compute the free energy barrier for a methyl transfer reaction catalyzed by the enzyme catechol O-methyltransferase at the level of density functional theory. The surrounding protein and solvent are found to have a profound effect on the reaction, and we show that energies can be extrapolated easily from one basis set and exchange-correlation functional to another. Using this procedure we calculate a barrier of 69 kJ/mol, in excellent agreement with the experimental value of 75 kJ/mol.