Dielectric fluctuations and the origins of noncontact friction

Dielectric fluctuations underlie a wide variety of physical phenomena, from ion mobility in electrolyte solutions and decoherence in quantum systems to dynamics in glass-forming materials and conformational changes in proteins. Here we show that dielectric fluctuations also lead to noncontact friction. Using high sensitivity, custom fabricated, single crystal silicon cantilevers we measure energy losses over poly(methyl methacrylate), poly(vinyl acetate), and polystyrene thin films. A new theoretical analysis, relating noncontact friction to the dielectric response of the film, is consistent with our experimental observations. This work constitutes the first direct, mechanical detection of noncontact friction due to dielectric fluctuations.     

Mössbauer effect in proteins

In proteins, the M?ssbauer effect and neutron scattering show a broad line and a rapid increase of the conformational mean-square displacement above about 180?K. The increase, dubbed the "dynamical transition," is controversial. We introduce a new interpretation of the M?ssbauer effect in proteins and demonstrate that no dynamical transition is required. The increase in the mean-square displacement and the broad line are caused by fluctuations in the protein's hydration shell. Using the dielectric spectrum of these fluctuations, we predict the shape of the M?ssbauer spectrum from 80 to 295?K with one dimensionless coefficient.     

Persistence of structure over fluctuations in biological electron-transfer reactions

In the soft-wet environment of biomolecular electron transfer, it is possible that structural fluctuations could wash out medium-specific electronic effects on electron tunneling rates. We show that beyond a transition distance (2-3 A in water and 6-7 A in proteins), fluctuation contributions to the mean-squared donor-to-acceptor tunneling matrix element are likely to dominate over the average matrix element. Even though fluctuations dominate the tunneling mechanism at larger distances, we find that the protein fold is "remembered" by the electronic coupling, and structure remains a key determinant of electron transfer kinetics.     

Flux of a Ratchet Model and Applications to Processive Motor Proteins

In this paper, we investigate the stationary probability current (or flux) of a Brownian ratchet model as a function of the flipping rate of the fluctuating potential barrier. It is shown that, with suitably selecting the parameters' values of the ratchet system, we can get the negative resonant activation, the positive resonant activation, the double resonant activation, and the current reversal, for the stationary probability current versus the flipping rate. The appearance of these phenomena is the result of the cooperative effects of the potential's dichotomous fluctuations and the internal thermal fluctuations on the evolution of the flux versus the flipping rate of the fluctuating potential barrier. In addition, some applications of our results to the motor proteins are discussed.     

Flux of a Ratchet Model and Applications to Processive Motor Proteins

In this paper, we investigate the stationary probability current(or flux) of a Brownian ratchet model as a function of the flipping rate of the fluctuating potential barrier. It is shown that, with suitably selecting the parameters' values of the ratchet system, we can get the negative resonant activation, the positive resonant activation,the double resonant activation, and the current reversal, for the stationary probability current versus the flipping rate.The appearance of these phenomena is the result of the cooperative effects of the potential's dichotomous fluctuations and the internal thermal fluctuations on the evolution of the flux versus the flipping rate of the fluctuating potential barrier. In addition, some applications of our results to the motor proteins are discussed.     

Motor proteins transporting cargos

Processive motor proteins such as kinesin and myosin-V are enzymes that use the energy of ATP hydrolysis to travel along polar cytoskeletal filaments. One of the functions of these proteins is the transport of vesicles and protein complexes that are linked to the light chains of the motors. Modeling the light chain by a linear elastic spring, and using the two-state model for one- and two-headed molecular motors, we study the influence of thermal fluctuations of the cargo on the motion of the motor-cargo complex. We solve numerically the Fokker-Planck equations of motor motion, and find that the mean velocity of the motor-cargo complex decreases monotonously as the spring becomes softer. This effect is due to the random force of thermal fluctuations of the cargo disrupting the operation of the motor. Increasing the size (thus, the friction coefficient) of the cargo also decreases the velocity. Surprisingly, we find that for a given size of the cargo, the velocity has a maximum for a certain friction of the motor. We explain this effect by the interplay between the characteristic length of thermal fluctuations of the cargo on a spring, the motor diffusion length, and the filament period. Our results may be relevant for the interpretation of single-molecule experiments with molecular motors (bead assays), where the motor motion is observed by tracking of a bead attached to the motor.     

Infrared spectroscopy and ultrasonic velocimetry as a tool for probing conformational flexibility of proteins

Abstract

Because of the crucial importance of structural fluctuations for function and stability of proteins, there is a strong interest for the relationships between structural fluctuations, the parameters of protein denaturation and the kinetics of H/D-exchange. Structural fluctuations can be described by volume and entropy fluctuations and these quantities are accessible via the isothermal compressibility, the thermal expansion and the isobaric heat capacity.

Our aim is to present the principal problem concerning the experimental procedures to answer those questions using lysozyme and α-lactalbumin. Whereas the transition parameters and the kinetics of the H/D-exchange were obtained using FTIR spectroscopy, the adiabatic compressibility was obtained by a combination of ultrasonic velocimetry and densitometry. It could be shown that the stability of the investigated proteins is correlated with reduced volume fluctuations. The expected direct correlation between H/D exchange rates and structural fluctuations could not be seen and it is assumed that the interactions are more complex than from the intuitive point of view.     

Maximum entropy with fluctuating constraints: The example of K-distributions

We indicate that in a maximum entropy setting, the thermodynamic β and the observation constraint are linked, so that fluctuations of the latter imposes fluctuations of the former. This gives an alternate viewpoint to ‘superstatistics’. While a Gamma model for fluctuations of the β parameter gives the so-called Tsallis distributions, we work out the case of a Gamma model for fluctuations of the observable, and show that this leads to K-distributions. We draw attention to the fact that these heavy-tailed distributions have high interest in physical applications, and we discuss them in some details.     

Time-dependent fluctuations and particle production in cosmological de Sitter and anti-de Sitter spaces

We study the evolution of time-dependent fluctuations and particle production in an expanding dS and contracting AdS universe. Using the functional Schrödinger formalism we are able to probe the time-dependent regime which is out of the reach of the standard approximations like the Bogolyubov method. In both cases, the evolution of fluctuations is governed by the harmonic oscillator equation with time-dependent frequency. In the case of an expanding dS universe we explicitly show that the frequency of fluctuations produced at a certain moment diminish in time, while the distribution of the created particles quickly approaches the thermal radiation of the dS space. In the case of a contracting AdS universe we show that the frequency of fluctuations produced at a certain moment grow in time. Nominally, the temperature of radiation diverges as the Big Crunch is approaching, however, increasing oscillations of the spectrum make the temperature poorly defined, which is in agreement with the fact that AdS space does not have an event horizon which would cause thermal radiation. Unlimited growth of fluctuations indicates that an eventual tunneling into AdS vacuum would have catastrophic consequences for our universe.     

On the Physical Origin of Long-Ranged Fluctuations in Fluids in Thermal Nonequilibrium States

Thermodynamic fluctuations in systems that are in nonequilibrium steady states are always spatially long ranged, in contrast to fluctuations in thermodynamic equilibrium. In the present paper we consider a fluid subjected to a stationary temperature gradient. Two different physical mechanisms have been identified by which the temperature gradient causes long-ranged fluctuations. One cause is the presence of couplings between fluctuating fields. Secondly, spatial variation of the strength of random forces, resulting from the local version of the fluctuation-dissipation theorem, has also been shown to generate long-ranged fluctuations. We evaluate the contributions to the long-ranged temperature fluctuations due to both mechanisms. While the inhomogeneously correlated Langevin noise does lead to long-ranged fluctuations, in practice, they turn out to be negligible as compared to nonequilibrium temperature fluctuations resulting from the coupling between temperature and velocity fluctuations.     

Reduction of magnetic field fluctuations in powered magnets for NMR using inductive measurements and sampled-data feedback control

Resistive and hybrid (resistive/superconducting) magnets provide substantially higher magnetic fields than those available in low-temperature superconducting magnets, but their relatively low spatial homogeneity and temporal field fluctuations are unacceptable for high resolution NMR. While several techniques for reducing temporal fluctuations have demonstrated varying degrees of success, this paper restricts attention to methods that utilize inductive measurements and feedback control to actively cancel the temporal fluctuations. In comparison to earlier studies using analog proportional control, this paper shows that shaping the controller frequency response results in significantly higher reductions in temporal fluctuations. Measurements of temporal fluctuation spectra and the frequency response of the instrumentation that cancels the temporal fluctuations guide the controller design. In particular, we describe a sampled-data phase-lead-lag controller that utilizes the internal model principle to selectively attenuate magnetic field fluctuations caused by the power supply ripple. We present a quantitative comparison of the attenuation in temporal fluctuations afforded by the new design and a proportional control design. Metrics for comparison include measurements of the temporal fluctuations using Faraday induction and observations of the effect that the fluctuations have on nuclear resonance measurements.     

Free energy self-averaging in protein-sized random heteropolymers

Current theories of heteropolymers are inherently macroscopic, but are applied to mesoscopic proteins. To compute the free energy over sequences, one assumes self-averaging--a property established only in the macroscopic limit. By enumerating the states and energies of compact 18, 27, and 36mers on a lattice with an ensemble of random sequences, we test the self-averaging approximation. We find that fluctuations in the free energy between sequences are weak, and that self-averaging is valid at the scale of real proteins. The results validate sequence design methods which exponentially speed up computational design and simplify experimental realizations.     

H模式放电中等离子体边界附近的漂移波不稳定性

本文从一简单模型出发,研究了H模式放电中边界附近的漂移波不稳定性。发现由于H模式放电中边界密度梯度很大,磁剪切的稳定作用变得不重要,漂移波不稳定性可以在边界附近发生,并可能成为宽频带密度涨落的原因。来自中性束加热的高能离子与漂移波的共振,则可能解释准相干涨落。     

Fluctuation-driven molecular transport through an asymmetric membrane channel

Channel proteins that selectively conduct molecules across cell membranes often exhibit an asymmetric structure. By means of a stochastic model, we argue that channel asymmetry in the presence of nonequilibrium fluctuations, fueled by the cell's metabolism as observed recently, can dramatically influence the transport through such channels by a ratchetlike mechanism. For an aquaglyceroporin that conducts water and glycerol, we show that a previously determined asymmetric glycerol potential leads to enhanced inward transport of glycerol, but for unfavorably high glycerol concentrations also to enhanced outward transport that protects a cell against poisoning.     

Study of the effect of director fluctuations on liquid-crystalline molecular reorientation

Initial phase of field-induced molecular reorientation in threshold geometry of a liquid-crystalline structure is essentially influenced by thermal orientational fluctuations. Still not quite clear is the way in which the reorientation starts and how it runs over an LC-structure in its initial phase. Fluctuations are stochastic events in time and also in space. This feature suggests, that the reorientation process may be induced by director fluctuations locally in a particular part of the LC-structure. In this work we have studied the impact of fluctuations on the molecular reorientation in nematics involving optical nonlinear interaction. The restricted area of a nematic layer was excited by light beam that amplified director fluctuations locally. By manipulation of optical excitation we were able to affect the dynamics of the effect. Since the threshold-type configuration of nematics is used in a number of optical devices, the obtained results may have practical aspect contributing to a new way of controlling the field-induced transition.     

Generalized Nagumo model: interesting effects of parameters’ fluctuations

In this paper, we used an analytical method to calculate the effects that produce the parameter’s fluctuations characterizing a generalization of Nagumo model. (The extinction option is replaced by one of low density homogeneous population.) Moreover, we also check the results by means of numerical simulations of the corresponding stochastic process. We find that these fluctuations have a strong impact on the solutions producing interesting changes.     

Survival probability and fluctuations in random trapping models

Through a very simple treatment we have constructed a lower bound for the statistical fluctuations of the survival probability of particles moving diffusively in a medium with random traps. We show that in the asymptotic regime the total survival probability is a non-self averaging quantity, in that the fluctuations dominate the mean value.     

Recent progress in the theory of itinerant electron magnetism

A review is given of recent theoretical investigations toward unified understanding of magnetism in narrow-band electron systems. It is emphasized that the classical controversy between the itinerant and localized models have been resolved into a more general and well-defined problem of spin density fluctuations in a general sense. The local moment picture is a limiting form of general spin fluctuations; and in its opposite limit we have weakly ferro- and antiferromagnetic metals. As an approach from the latter limit, the self-consistent renormalization theory of spin fluctuations is shown to have been quite successful in explaining and predicting a number of qualitatively new physical properties of this class of materials. More recent theoretical studies of spin fluctuations from a general point of view interpolating between the above-mentioned two limits seem to lead to a unified picture of magnetism in narrow-band electron systems including 3d transition metals and magnetic compounds.     

Pressure and protein dynamism

The dynamism of life depends critically on the dynamism of bio-macromolecules themselves, notably proteins. The bio-macromolecular dynamism originates from weak non-bonding interactions, which inevitably fluctuate under physiological conditions. The fascination lies in the fact that, in proteins, the basically random “non-biological fluctuations” of atoms are often turned into specific “biological fluctuations” of larger amplitude, which would be directly coupled to protein function and consequently the dynamism of life such as growth, motility, sensing, adaptation and disease. The success of the combination of pressure perturbation with advanced nuclear magnetic resonance (NMR) spectroscopy by using the online cell method has provided a powerful means for investigating details of such “biological fluctuations”, which encompass, in general, a much wider conformational space of a protein than hitherto explored. Some representative strategies of high pressure NMR spectroscopy for characterizing protein dynamism will be discussed with actual examples.