Direct observation of large temperature fluctuations during DNA thermal denaturation

Fluctuations of thermal variables investigated by cross-correlation function

Fluctuations in conjugate thermodynamic variables are studied using the cross-correlation function. A new procedure is given enabling the derivation of fluctuation formulas for a system in equilibrium. Specifically, the cross-correlation function between heat and temperature is employed for thermal variables. Additionally, fluctuation-dissipation relations involving the frequency-dependent specific heat are established. Moreover, a general relation concerning the average entropy production is also given, which is the microscopic analog of the dissipation formula of the linear response theory. In the case of thermal variables, this formula finds application in various scenarios describing fluctuating thermal systems in equilibrium.

Absolute calibration of the latent heat of transition using differential thermal analysis

We describe a simple and accurate differential thermal analysis setup to measure the latent heat of solid state materials undergoing abrupt phase transitions in the temperature range from 77 K to above room temperature. We report a numerical technique for the absolute calibration of the latent heat of transition without the need for a reference sample. The technique is applied to three different samples-vanadium sesquioxide undergoing the Mott transition, bismuth barium ruthenate undergoing a magnetoelastic transition, and an intermetallic Heusler compound. In each case, the inferred latent heat value agrees with the literature value within its error margins. To further demonstrate the importance of absolute calibration, we show that the changes in the latent heat of the Mott transition in vanadium sesquioxide (V₂O₃) remain constant to within 2% even as the depth of supersaturation changes by about 10 K in non-equilibrium dynamic hysteresis measurements. We also apply this technique for the measurement of the temperature-dependent specific heat.

Kinetic Spinodal Instabilities in the Mott Transition in V_{2}O_{3}: Evidence from Hysteresis Scaling and Dissipative Phase Ordering

We present the first systematic observation of scaling of thermal hysteresis with the temperature scanning rate around an abrupt thermodynamic transition in correlated electron systems. We show that the depth of supercooling and superheating in vanadium sesquioxide (V_{2}O_{3}) shifts with the temperature quench rates. The dynamic scaling exponent is close to the mean field prediction of 2/3. These observations, combined with the purely dissipative continuous ordering seen in "quench-and-hold" experiments, indicate departures from classical nucleation theory toward a barrier-free phase ordering associated with critical dynamics. Observation of critical-like features and scaling in a thermally induced abrupt phase transition suggests that the presence of a spinodal-like instability is not just an artifact of the mean field theories but can also exist in the transformation kinetics of real systems, surviving fluctuations.

Molecular rigidity and enthalpy-entropy compensation in DNA melting

Enthalpy-entropy compensation (EEC) is observed in diverse molecular binding processes of importance to living systems and manufacturing applications, but this widely occurring phenomenon is not sufficiently understood from a molecular physics standpoint. To gain insight into this fundamental problem, we focus on the melting of double-stranded DNA (dsDNA) since measurements exhibiting EEC are extensive for nucleic acid complexes and existing coarse-grained models of DNA allow us to explore the influence of changes in molecular parameters on the energetic parameters by using molecular dynamics simulations. Previous experimental and computational studies have indicated a correlation between EEC and changes in molecular rigidity in certain binding-unbinding processes, and, correspondingly, we estimate measures of DNA molecular rigidity under a wide range of conditions, along with resultant changes in the enthalpy and entropy of binding. In particular, we consider variations in dsDNA rigidity that arise from changes of intrinsic molecular rigidity such as varying the associative interaction strength between the DNA bases, the length of the DNA chains, and the bending stiffness of the individual DNA chains. We also consider extrinsic changes of molecular rigidity arising from the addition of polymer additives and geometrical confinement of DNA between parallel plates. All our computations confirm EEC and indicate that this phenomenon is indeed highly correlated with changes in molecular rigidity. However, two distinct patterns relating to how DNA rigidity influences the entropy of association emerge from our analysis. Increasing the intrinsic DNA rigidity increases the entropy of binding, but increases in molecular rigidity from external constraints decreases the entropy of binding. EEC arises in numerous synthetic and biological binding processes and we suggest that changes in molecular rigidity might provide a common origin of this ubiquitous phenomenon in the mutual binding and unbinding of complex molecules.

1/ f noise from the laws of thermodynamics for finite-size fluctuations

Computer simulations of the Ising model exhibit white noise if thermal fluctuations are governed by Boltzmann's factor alone; whereas we find that the same model exhibits 1/f noise if Boltzmann's factor is extended to include local alignment entropy to all orders. We show that this nonlinear correction maintains maximum entropy during equilibrium fluctuations. Indeed, as with the usual way to resolve Gibbs' paradox that avoids entropy reduction during reversible processes, the correction yields the statistics of indistinguishable particles. The correction also ensures conservation of energy if an instantaneous contribution from local entropy is included. Thus, a common mechanism for 1/f noise comes from assuming that finite-size fluctuations strictly obey the laws of thermodynamics, even in small parts of a large system. Empirical evidence for the model comes from its ability to match the measured temperature dependence of the spectral-density exponents in several metals and to show non-Gaussian fluctuations characteristic of nanoscale systems.

Glassy Interfacial Dynamics of Ni Nanoparticles: Part II Discrete Breathers as an Explanation of Two-Level Energy Fluctuations

Recent studies of the dynamics of diverse condensed amorphous materials have indicated significant heterogeneity in the local mobility and a progressive increase in collective particle motion upon cooling that takes the form of string-like particle rearrangements. In a previous paper (Part I), we examined the possibility that fluctuations in potential energy E and particle mobility μ associated with this 'dynamic heterogeneity' might offer information about the scale of collective motion in glassy materials based on molecular dynamics simulations of the glassy interfacial region of Ni nanoparticles (NPs) at elevated temperatures. We found that the noise exponent associated with fluctuations in the Debye-Waller factor, a mobility related quantity, was directly proportional to the scale of collective motion L under a broad range of conditions, but the noise exponent associated with E(t) fluctuations was seemingly unrelated to L. In the present work, we focus on this unanticipated difference between potential energy and mobility fluctuations by examining these quantities at an atomic scale. We find that the string atoms exhibit a jump-like motion between two well-separated bands of energy states and the rate at which these jumps occur seems to be consistent with the phenomenology of the 'slow-beta' relaxation process of glass-forming liquids. Concurrently with these local E(t) jumps, we also find 'quake-like' particle displacements having a power-law distribution in magnitude so that particle displacement fluctuations within the strings are strikingly different from local E(t) fluctuations. An analysis of these E(t) fluctuations suggests that we are dealing with 'discrete breather' excitations in which large energy fluctuations develop in arrays of non-linear oscillators by virtue of large anharmonicity in the interparticle interactions and discreteness effects associated with particle packing. We quantify string collective motions on a fast caging times scale (picoseconds) and explore the significance of these collective motions for understanding the Boson peak of glass-forming materials.

Colored noise in the fluctuations of an extended DNA molecule detected by optical trapping

We studied fluctuations of an optically trapped bead connected to a single DNA molecule anchored between the bead and a cover glass or between two optically trapped beads. Power spectral densities of the bead position for different extensions of the molecule were compared with the power spectral density of the position fluctuations of the same bead without the molecule attached. Experiments showed that the fluctuations of the DNA molecule extended up to 80% by a force of 3 pN include the colored noise contribution with spectral dependence 1/f (α) with α ~ 0.75.

Thermal fluctuation spectroscopy of DNA thermal denaturation

We have developed the technique of thermal fluctuation spectroscopy to measure the thermal fluctuations in a system. This technique is particularly useful to study the denaturation dynamics of biomolecules like DNA. Here we present a study of the thermal fluctuations during the thermal denaturation (or melting) of double-stranded DNA. We find that the thermal denaturation of heteropolymeric DNA is accompanied by large, non-Gaussian thermal fluctuations. The thermal fluctuations show a two-peak structure as a function of temperature. Calculations of enthalpy exchanged show that the first peak comes from the denaturation of AT rich regions and the second peak from denaturation of GC rich regions. The large fluctuations are almost absent in homopolymeric DNA. We suggest that bubble formation and cooperative opening and closing dynamics of basepairs causes the additional fluctuation at the first peak and a large cooperative transition from a partially molten DNA to a completely denatured state causes the additional fluctuation at the second peak.

1/f fluctuations of DNA temperature at thermal denaturation

We theoretically investigated the temperature fluctuations of DNA close to denaturation and observed a strong enhancement of these fluctuations at the critical temperature. Although in a much lower frequency range, such a sharp increase was also reported in the recent experimental work of Nagapriya [Phys. Rev. Lett. 96, 038102 (2006)]. We showed that there is instead no enhancement of temperature fluctuations when the dissipation coefficient gamma in Langevin equations is assumed to be larger than a few tens of ps;{-1} , and pointed out the possible role of the solvent in real experiments. We sought for a possible correlation between the growth of large bubbles and the enhancement of temperature fluctuations but found no direct evidence thereof. Finally, we showed that neither the enhancement of fluctuations nor the 1f dependence are observed at the scale of a single base pair, while these properties show up when summing the contributions of a large number of base pairs. We therefore conclude that both effects result from collective motions that are facilitated by the divergence of the correlation length at denaturation.