Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality

Recent advances in statistical mechanical theory can be used to solve a fundamental problem in experimental thermodynamics. In 1997, Jarzynski proved an equality relating the irreversible work to the equilibrium free energy difference, DeltaG. This remarkable theoretical result states that it is possible to obtain equilibrium thermodynamic parameters from processes carried out arbitrarily far from equilibrium. We test Jarzynski's equality by mechanically stretching a single molecule of RNA reversibly and irreversibly between two conformations. Application of this equality to the irreversible work trajectories recovers the DeltaG profile of the stretching process to within k(B)T/2 (half the thermal energy) of its best independent estimate, the mean work of reversible stretching. The implementation and test of Jarzynski's equality provides the first example of its use as a bridge between the statistical mechanics of equilibrium and nonequilibrium systems. This work also extends the thermodynamic analysis of single molecule manipulation data beyond the context of equilibrium experiments.     

木材的热力学函数

从木材的微观结构出发，并把木材视为一个热力学系统。应用晶态固体理论和热力学关系，在木材比热容理论表达式的基础上，导出了木材的状态方程，内能，熵等热力学函数。     

Neutron-mapping polymer flow: scattering, flow visualization, and molecular theory

Flows of complex fluids need to be understood at both macroscopic and molecular scales, because it is the macroscopic response that controls the fluid behavior, but the molecular scale that ultimately gives rise to rheological and solid-state properties. Here the flow field of an entangled polymer melt through an extended contraction, typical of many polymer processes, is imaged optically and by small-angle neutron scattering. The dual-probe technique samples both the macroscopic stress field in the flow and the microscopic configuration of the polymer molecules at selected points. The results are compared with a recent "tube model" molecular theory of entangled melt flow that is able to calculate both the stress and the single-chain structure factor from first principles. The combined action of the three fundamental entangled processes of reptation, contour length fluctuation, and convective constraint release is essential to account quantitatively for the rich rheological behavior. The multiscale approach unearths a new feature: Orientation at the length scale of the entire chain decays considerably more slowly than at the smaller entanglement length.     

The mechanisms of irreversible enzyme inactivation at 100C

The mechanism of irreversible thermoinactivation of an enzyme has been quantitatively elucidated in the pH range relevant to enzymatic catalysis. The processes causing irreversible inactivation of hen egg-white lysozyme at 100 degrees C are deamidation of asparagine residues, hydrolysis of peptide bonds at aspartic acid residues., destruction of disulfide bonds, and formation of incorrect (scrambled) structures; their relative contributions depend of the pH.     

一类不可逆奥托循环性能的优化分析

应用有限时间热力学方法,导出一类不可逆奥托循环的输出功和效率与不可逆绝热因子、压缩比、高低温比之间的关系,分析绝热过程的不可逆性对奥托循环性能参数的影响.所得结果可为实际热机的优化设计和性能改善提供一些新的理论依据.     

Brownian motion and nonequilibrium statistical mechanics

This article is a personal reflection of the branch of nonequilibrium statistical mechanics called the linear response theory that has as its heart the fluctuation-dissipation thereom, which states that irreversible processes ip nonequilibrium are necessarily related to thermal fluctuations in equilibrium. Its origi lies in the Einstein relation for the diffusion constant and the mobility of a Brownian particle. The short history of the fluctuation-dissipation theorem is described. Then the linear response theory is brifly summarized and the meaning of stochastization is considered. The Langevin equation approach and its extensions are reviewed.     

Tenuous structures from disorderly growth processes

Colloidal aggregation and other random growth processes produce structures that behave differently from ordinary bulk matter. Much of this behavior can be described in terms of the invariance of the aggregates under changes of spatial length scale: they appear to be fractals. There are two types of basic mechanisms for producing fractal aggregates. Those in which aggregation proceeds cluster by cluster can be understood qualitatively in terms of a solvable schematic model. The diffusion-limited aggregation or deposition of individual particles to make a large cluster is not as well understood. It is closely related to several irreversible processes in other areas of physics, such as two-fluid displacement in porous materials and the dielectric breakdown of insulators. More generally, disorderly growth mechanisms provide structures having unique properties, many of which can be understood by using simple statistical principles.     

Measurement structures and psychological laws

Empirical laws psychology may be based on physical measurements (for example, voltages, times), counting, ordering, or just classifying. It is a pointless, though widespread practice to use a physical measure or a count as a "definition" of a psychological variable; this practice obscures the fact that all one has done is measured a physical variable, or counted. What is important are the empirical laws that are established by use of such quantitative or qualitative observations. Some kinds of empirical relations and laws yield measurement structures, akin to the qualitative structures underlying fundamental measurement in physics. Measurement structures are empirical structures that can be described most simply by introduction of a new numerical function; such a function is a new measure, and is typically interpreted as measuring some particular psychological variable Measurement structures, formulated abstractly, sometimes provide valuable tools for formulating new empirical hypotheses to be tested; but in many instances, other kinds of theory may be more appropriate. The main focus of research ought always to be the discovery of simple laws; these may or may not lead to new measures.     

Dendrites, viscous fingers, and the theory of pattern formation

There has emerged recently a new theoretical picture of the way in which patterns are formed in dendritic crystal growth and in the closely analogous phenomenon of viscous fingering in fluids. Some interesting questions that arise in connection with this theory include: How broad is its range of validity? How do we understand dynamic stability in systems of this kind? What is the origin of sidebranches? Can weak noise, or even microscopic thermal fluctuations, play a role in determining the macroscopic features of these systems?     

木材弦向导温系数的理论研究

以细长中空的同轴圆柱体作为木材生物学细胞模型,以4个D吡喃葡萄糖基组成单斜晶系的晶胞作为木材纤维结构的微观模型,综合应用木材物理学、统计热力学和结构化学等多个学科的基础理论和方法,研究推导木材弦向导温系数的理论表达式,应用该表达式实际计算了24种不同树种的木材弦向导温系数,并与同条件下的实验值相比较,其结果为最大误差12．2％,平均误差7．1％。     

Cilia in nematode sensory organs

Electron microscopic studies revealed thle presenlce of true cilia in nerve processes connected with sensory organs of a nemnatodes. These structures are important in evaluating the relation between nematodes and the other aschelminths, from which they were separated partially on the basis of the supposed total absence of cilia.     

Early Archaean microorganisms preferred elemental sulfur, not sulfate

Microscopic sulfides with low 34S/32S ratios in marine sulfate deposits from the 3490-million-year old Dresser Formation, Australia, have been interpreted as evidence for the presence of early sulfate-reducing organisms on Earth. We show that these microscopic sulfides have a mass-independently fractionated sulfur isotopic anomaly (Delta33S) that differs from that of their host sulfate (barite). These microscopic sulfides could not have been produced by sulfate-reducing microbes, nor by abiologic processes that involve reduction of sulfate. Instead, we interpret the combined negative delta34S and positive Delta33S signature of these microscopic sulfides as evidence for the early existence of organisms that disproportionate elemental sulfur.     

用常压储罐和高压储罐联合储存LNG

介绍了液化天然气(LNG)升压后的自冷热力学特性,指出了LNG的储存方式及存在的问题.根据LNG的热力学特性,提出了利用高压储罐和常压储罐相结合的方法储存LNG.该方法需要的设备少、工艺简单、易于操作、投资少、适用范围广,是一种新型、有效的LNG储存方法,具有推广应用价值.     

Optical matter: crystallization and binding in intense optical fields

Properly fashioned electromagnetic fields coupled to microscopic dielectric objects can be used to create arrays of extended crystalline and noncrystalline structures. Organization can be achieved in two ways: In the first, dielectric matter is transported in direct response to the externally applied standing wave optical fields. In the second, the external optical fields induce interactions between dielectric objects that can also result in the creation of complex structures. In either case, these new ordered structures, whose existence depends on the presence of both light and polarizable matter, are referred to as optical matter.     

Theoretical chemistry comes alive: full partner with experiment

During the last decade, advances in computational techniques and in the extraction of chemically useful concepts from electronic wave functions have put theorists into the mainstream of chemistry. Some recent examples of the prediction of spectroscopic quantities and the elucidation of catalytic processes for homogeneous and heterogeneous reactions from theoretical calculations are used to illustrate how theory and experiment are now full partners in chemical research. It is expected that during the next decade the thrust of theoretical chemistry will be to combine the knowledge of fundamental chemical steps and fundamental interactions with advances in chemical dynamics and irreversible statistical mechanics and in computer technology to produce simulations of chemical systems with competing reactions taking place simultaneously at various reaction sites. The promise of such simulation is illustrated by a study of the enzyme thermolysin.     

Phonon optics and phonon propagation in semiconductors

Recent experiments involving the propagation of extremely high frequency, short-wavelength acoustic phonons in semiconductors are described. Such phonons, which play an important role in thermal energy transpor and nonradiative recombination processes, can be used as sensitive microscopic probes of electronic, defect, and interface states. Experiments on phonon transmission thrugh epitaxially grown bulk material as well as thin-film superlattice structures in the semiconductor gallium arsenide are described. Such thin-film periodic structures can be used to build frequency-selective phonon filters and reflectors, which can in turn be used to manipulate phonon diagnostic beams in technologically important materials.     

Steady-state coupling of ion-channel conformations to a transmembrane ion gradient

Under stationary conditions, opening and closing of single Torpedo electroplax chloride channels show that the number of transitions per unit time between inactivated and conducting states are unequal in opposite directions. This asymmetry, which increases with transmembrane electrochemical gradient for the chloride ion, violates the principle of microscopic reversibility and thus demonstrates that the channel-gating process is not at thermodynamic equilibrium. The results imply that the channel's conformational states are coupled to the transmembrane electrochemical gradient of the chloride ion.     

Observation of transient structural-transformation dynamics in a Cu2S nanorod

The study of first-order structural transformations has been of great interest to scientists in many disciplines. Expectations from phase-transition theory are that the system fluctuates between two equilibrium structures near the transition point and that the region of transition broadens in small crystals. We report the direct observation of structural fluctuations within a single nanocrystal using transmission electron microscopy. We observed trajectories of structural transformations in individual nanocrystals with atomic resolution, which reveal details of the fluctuation dynamics, including nucleation, phase propagation, and pinning of structural domains by defects. Such observations provide crucial insight for the understanding of microscopic pathways of phase transitions.     

Molecular and Biochemical Aspects of the Ontogenesis of Eukaryotes Under Global Warming

Global warming is an irreversible process resulting in the deterioration of living conditions for various organisms, including the most important agricultural species. So-called σ32 factor of Escherichia coli is embedded into the RNA thermosensor in the λ cIII gene and plays an important role in the regulation of bacterial response to heightened temperatures. Expression of heat/cold shock genes and some virulence genes in response to temperature changes is coordinated by the genome. There are some known RNA thermosensors with different structures that provide a functional control of the diversity of cellular processes. The most common RNA thermosensor is the ROSE element suppressing expression of heat shock genes. A common feature of all ROSE elements is the presence of the G residue opposite to the SD sequence since this nucleotide is functionally important and its elimination makes the RNA thermosensor insensitive to high temperatures. In this paper, we describe molecular sequences (RNA thermosensors) whose chemical compounds influence on the homeostatic temperature regulation, namely, on the corresponding enzymes. Though the data on RNA thermosensors were obtained for microorganisms, it may be possible in the long run to change the animal genome at the molecular level by the insertion of these sequences or cultivation of symbiotic microorganisms, which may be used for production of biologically active compounds. In addition, such insertions would probably be able to reduce the negative effect of high environmental temperatures on living organisms.