The convergence properties of the absolute single-molecule configurational entropy and the correction terms used to estimate it are investigated using microsecond molecular dynamics simulation of a peptide test system and an improved methodology. The results are compared with previous applications for systems of diverse chemical ...

... the square root of the mean number of centers in resonance. To be precise, defining the ... absorption profile scaling in absolute magnitude as ,/N,. ...

... Use of silicon carbide thin films is hampered, however ... to reproducibly grow stoichiometric films free from ... is that absolutely reproducible flows of the ...

... Use of silicon carbide thin films is hampered, however ... to reproducibly grow stoichiometric films free from ... is that absolutely reproducible flows of the ...

Surfaces and Orientations: Much to FRET about? IVAN RASNIK, SEAN A. MCKINNEY, AND TAEKJIP HA-Champaign, Urbana, Illinois 61801 Received August 17, 2004 ABSTRACT Single molecule FRET (fluorescence resonance single molecule FRET time trajectories with or without absolute distance information. ...

Prigogine's Principle of Minimum Entropy Production'', as well as the complementary maximum entropy production principle were examined from a more basic point of view. Two theorems are provided: absolute maximum entropy configurations can be considered to timedevelop from ...

In recent years, laser induced fluorescence detection and spectroscopy of single molecules (SMD) has seen a tremendous development. Besides fundamental research on individual molecular systems, practical applications of this sensitive detection technique for analytical and diagnostic purposes are becoming more and more important. For a wider applicability ...

... with μ the chemical potential for vacancy diffusion. The Helmholtz free energy � , specific entropy η , and absolute temperature θ are related by ...

Single molecule fluorescence measurements provide detailed information about sub-populations, transition intermediates and kinetic data for systems that are not able to be synchronized by removing the ensemble average. One commonly used fluorescence technique is single molecule Foerster Resonance Energy Transfer ...

More sensitive techniques in molecular and clinical immunology are essential for the development of reproducible profiles. We have developed a novel methodology named solution-phase single-molecule fluorescence correlation spectroscopy (SPSM-FCS) that fulfils these demands. It is based on the quantification of the probability density of single ...

Considering the contribution of both the outer and inner horizons, the Hamilton-Jacobi method is applied to a Kerr-Newman black hole and a negative temperature of the inner horizon is obtained. Under the negative temperature inside the black hole, the thermodynamics of the two horizons is studied, and the new Bekenstein-Smarr formula is given. The entropies of the inner and ...

In this review, we describe technology and use of single-fluorophore imaging and detection in living cells with regard to application in systems biology and medicine. Because all biological reactions occur under aqueous conditions, the realization of single-fluorophore imaging using an optical microscope has led to the direct observation of biological molecules at work. Today, we can observe ...

We have developed an experimental platform to control and modify the DNA on a DNA-Single Walled Nanotube (SWNT) complex for the purpose of detecting labeled and unlabeled protein-DNA interactions via visible fluorescence. By exploiting the distance-dependent photophysical interaction between organic fluorophores and the surface of a SWNT as the sensing mechanism, fluorophore-conjugated DNA-SWNTs ...

The binding of proteins and ligands is generally associated with the loss of translational, rotational and conformational entropy. In many cases, however, the net entropy change due to binding is positive. To develop a deeper understanding of the energetics of entropically driven protein-ligand binding, we calculated the absolute ...

Data are tabulated for the thermodynamic properties of sodium at saturated pressures at 426 to 1856.3 deg K and in the superheated region at 426 to 2600 deg K for pressures of 10-/sup 8/ to 50 atm absolute. The temperature- entropy chart covers the regions 200 to 4200 deg F and 0 to 3.3 entropy units. A specific volume as a ...

Three recent applications of maximal entropy procedures to models of turbulence in plasmas are described. They are: (1) the calculation of most probable states in guiding-center plasmas and vortex fluids; (2) the calculation of most probable magnetohydrodynamic equilibrium profiles; and (3) the prediction of absolute equilibrium Gibbs ensemble spectra for ...

This paper discusses how the Carnot engine led to the formulation of the second law of thermodynamics and entropy. The operation of the engine is analysed both in terms of heat as the caloric fluid and heat as a form of energy. A keystone of Carnot's thinking was the absolute conservation of caloric. Although the Carnot analysis was partly incorrect, ...

This paper discusses how the Carnot engine led to the formulation of the second law of thermodynamics and entropy. The operation of the engine is analysed both in terms of heat as the caloric fluid and heat as a form of energy. A keystone of Carnot's thinking was the absolute conservation of caloric. Although the Carnot analysis was partly incorrect, ...

Traditional diversity measures such as the Shannon entropy are generally computed from the species' relative abundance vector of a given community to the exclusion of species' absolute abundances. In this paper, I first mention some examples where the total information content associated with a given community may be more adequate than Shannon's average ...

Recent developments of single molecule detection techniques and in particular the introduction of fluorescence correlation spectroscopy (FCS) led to a number of important applications in biological research. We present a unique approach for the gene expression analysis using dual-color cross-correlation. The expression assay is based on gene-specific ...

We present a model of non-specific cooperative binding of proteins to DNA in which the binding of isolated proteins generates local bends but binding of proteins at neighboring sites on DNA straightens the polymer. We solve the statistical mechanical problem and calculate the effective persistence length, site occupancy and cooperativity. Cooperativity leads to non-monotonic variation of the ...

We present an outlook on the climate system thermodynamics. First, we construct an equivalent Carnot engine with efficiency eta and frame the Lorenz energy cycle in a macroscale thermodynamic context. Then, by exploiting the second law, we prove that the lower bound to the entropy production is eta times the integrated absolute value of the internal ...

We present an outlook on the climate system thermodynamics. First, we construct an equivalent Carnot engine with efficiency ? and frame the Lorenz energy cycle in a macroscale thermodynamic context. Then, by exploiting the second law, we prove that the lower bound to the entropy production is ? times the integrated absolute value of the internal ...

We implement a unique strategy for single molecule counting termed stochastic labeling, where random attachment of a diverse set of labels converts a population of identical DNA molecules into a population of distinct DNA molecules suitable for threshold detection. The conceptual framework for stochastic labeling is developed and experimentally ...

... Single-Molecule Luminescence and High Efficiency Photovoltaic Cells Based on ... novel optoelectronic materials that exploit single-molecule effects. ...

electrophoresis, flow cytometry, DNA fingerprinting, fragment sizing sequencing. Proper application of the single molecule fluorescence techniques in these ...

... The long-term goal of this project is to develop transistors and switches based on single molecules. Since transistors and ...

Any theory with definite causal structure has a defined past and future, be it defined by light cones or an absolute time scale. Entropy is a concept that has traditionally been reliant on a definite notion of causality. However, without a definite notion of causality, the concept of entropy is not all lost. Indefinite causal structure ...

Sacrificial bonds and hidden length in structural molecules and composites have been found to greatly increase the fracture toughness of biomaterials by providing a reversible, molecular-scale energy-dissipation mechanism. This mechanism relies on the energy, of order 100 eV, needed to reduce entropy and increase enthalpy as molecular segments are stretched after being ...

Enzymes reside on a convoluted free energy surface. This free energy surface generates the conformational dynamics that control activity. We use single molecule F�rster Resonance Energy Transfer measurements to study these conformational dynamics and the physics that underly them in a model enzyme, Adenylate Kinase (AK), which catalyzes the ...

A method of statistical estimation is applied to the problem of evaluating the absolute entropy of internal rotation in a molecule with two torsional degrees of freedom. The configurational part of the entropy is obtained as that of the joint probability density of an arbitrary form represented by a two-dimensional Fourier series, the ...

Transition paths are a uniquely single-molecule property not yet observed for any molecular process in solution. The duration of transition paths is the tiny fraction of the time in an equilibrium single-molecule trajectory when the process actually happens. Here, we report the determination of an upper bound for the transition path time for protein ...

... 23, 833, 1937). T = absolute temperature S = entropy U = internal energy, H is the applied field. The Helmholtz free energy is 0 F = fo(T)V - roIdHo ...

Let X be a random variable with an absolutely continuous distribution function, and (Uk) be a sequence of random variables, independent of X, whose r-th mean converges to zero. Then it is shown that the existence of the R-th mean of X, for some positive R...

... 5 r : heat source per unit mass (ie, radiation) e � θη = - : Helmholtz free energy per unit mass θ : absolute temperature η : entropy per unit mass ...

The entropy and the light-induced valence tautomeric interconversions of solid solutions of the [Co(Me(2)tpa)(diox)](PF(6)).C(6)H(5)CH(3) complex [Me(2)tpa = bis(6-methyl-(2-pyridylmethyl))(2-pyridylmethyl)amine and diox = catecholato (DBCat) or semiquinonato (DBSQ) forms of 3,5-ditert-butylquinone] in the electronically innocent [Zn(Me(2)tpa)(DBSQ)](PF(6)).C(6)H(5)CH(3) host, ...

Employing an extended version of the Boltzmann-Uehling-Uhlenbeck equation, we present simulations of the reaction 800 MeV/nucleon Ca+Ca. Deuteron spectra are calculated from the model without ad hoc assumptions. Absolute values of the proton and deuteron spectra are in good agreement with experiment. The dependence of the total deuteron yield on the nuclear equation of state ...

It is shown that time and entropy operators may exist as superoperators in the framework of the Liouville space provided that the Hamiltonian has an unbounded absolutely continuous spectrum. In this case the Liouville operator has uniform infinite multiplicity and thus the time operator may exist. A general proof of the Heisenberg uncertainty relation ...

By means of a variant approach to Standard Relativistic Cosmology, we hint that the entropy of the Universe is growing with t 3/2, where t stands for time-coordinate. Then, the absolute temperature obeys Standard t -1/2-dependence. We make contact with our previous paper (Berman, Int. J. Theor. Phys., 2009), in the context of a Machian Universe; but we ...

A new statement of the second law of thermodynamics is given. The law leads almost effortlessly, for very general closed systems, to a definition of absolute entropy S, a demonstration that ΔS>0 in adiabatic processes, a definition of temperature, and a demonstration that dS>δQ/T in quasistatic processes. ...

We review with a tutorial scope the information theory foundations of quantum statistical physics. Only a small proportion of the variables that characterize a system at the microscopic scale can be controlled, for both practical and theoretical reasons, and a probabilistic description involving the observers is required. The criterion of maximum von Neumann entropy is then ...

In contrast to most other thermodynamic data, entropy values are not given in relation to a certain--more or less arbitrarily defined--zero level. They are listed in standard thermodynamic tables as absolute values of specific substances. Therefore these values describe a physical property of the listed substances. One of the main tasks of chemistry is to ...

We have recently applied the second law to an isolated system, consisting of a system {\\Sigma} such as a glass surrounded by an extremely large medium {\\Sigma}, to show that the instantaneous temperature T(t), thermodynamic entropy S(T_0,t) and enthalpy H(T_0,t) of {\\Sigma} decrease in any isothermal relaxation towards their respective equilibrium values under isobaric ...

We develop a general minimally coupled subspace approach (MCSA) to compute absolute entropies of macromolecules, such as proteins, from computer generated canonical ensembles. Our approach overcomes limitations of current estimates such as the quasi-harmonic approximation which neglects non-linear and higher-order correlations as well as multi-minima ...

In recent years, theories of nonequilibrium statistical mechanics such as the fluctuation theorem (FT) and the Jarzynski equality have been experimentally applied to micro and nanosized systems. However, so far, these theories are seldom applied to autonomous systems such as motor proteins. In particular, representing the property of entropy production in a small system driven ...

Recent data increasingly reveal that conformational dynamics are indispensable to enzyme function throughout the catalytic cycle, in substrate recruiting, chemical transformation, and product release. Conformational transitions may involve conformational selection and induced fit, which can be viewed as a special case in the catalytic network. NMR, X-ray crystallography, ...

We report data for the single molecule conductance of (a) photochromic molecules in the `open' and `closed' forms and (b) carotenoid polyenes. The photochromic molecules we studied switch between an open state (that absorbs in the UV to become closed) and a closed state (that absorbs in the visible to become open) through light-induced isomerization. The ...

-mail: nuria.agell@esade.edu Abstract A new concept of generalized absolute orders of magnitude qualitative of absolute orders of magnitude and with the classical interval algebra. In addition, the al- gebraic results. To this end, the mathematical struc- tures of Orders of Magnitude Qualitative Spaces (OM) were

The monitoring of anesthetic depth is an absolutely necessary procedure in the process of surgical operation. To judge and control the depth of anesthesia has become a clinical issue which should be resolved urgently. EEG collected wiil be processed by sort entrop in this paper. Signal response of the surface of the cerebral cortex is determined for different stages of ...

1. Investigations that assess cardiac autonomic function include non-linear techniques such as fractal dimension and approximate entropy in addition to the common time and frequency domain measures of both heart period and heart rate. This article evaluates the differences in using heart rate versus heart period to estimate fractal dimensions and approximate ...

Structural assembly is critical to RNA biological functionality. However, an energetic and molecular description of how RNA folds pales in comparison to the understanding of protein folding. To gain molecular insight into the energetic barriers along RNA folding pathways, we explore the transition states for an elementary folding step by extracting the enthalpy and entropy ...

RNA folding thermodynamics are crucial for structure prediction, which requires characterization of both enthalpic and entropic contributions of tertiary motifs to conformational stability. We explore the temperature dependence of RNA folding due to the ubiquitous GAAA tetraloop�receptor docking interaction, exploiting immobilized and freely diffusing single-molecule ...

Stark Effect on Single Molecules of Dibenzanthanthrene in a Naphthalene Crystal and in a n on centrosymmetric dibenzanthanthrene molecules in naphthalene, a centrosymmetric crystal, where it is mainly Stark effect measurements on single molecules of dibenzanthanthrene (DBATT) in naphthalene crystals20

Phase I conclusively showed the feasibility of rational design of single molecule-source reagents that could lead to improvements in the chemical vapor deposition of stoichiometric Beta silicon carbide. Four single molecule sources were synthesized, their...