Understanding temperature-modulated calorimetry through studies of a model system.

Temperature modulated calorimetry is widely used but still raises some fundamental questions. In this paper we study a model system as a test sample to address some of them. The model has a nontrivial spectrum of relaxation times.

Melting transition of oriented Li-DNA fibers submerged in ethanol solutions.

The melting transition of Li-DNA fibers immersed in ethanol-water solutions has been studied using calorimetry and neutron diffraction techniques. The data have been analyzed using the Peyrard-Bishop-Dauxois model to determine the strengths of the intra- and inter-base pair potentials. The data and analysis show that the potentials are weaker than those for DNA in water.

Memory effects in glasses: Insights into the thermodynamics of out-of-equilibrium systems revealed by a simple model of the Kovacs effect.

Glasses are interesting materials because they allow us to explore the puzzling properties of out-of-equilibrium systems. One of them is the Kovacs effect in which a glass, brought to an out-of-equilibrium state in which all its thermodynamic variables are identical to those of an equilibrium state, nevertheless evolves, showing a hump in some global variable before the thermodynamic variables come back to their starting point. We show that a simple three-state system is sufficient to study this phenomenon using numerical integrations and exact analytical calculations.

How is information transmitted in a nerve?

In the last 15 years, a debate has emerged about the validity of the famous Hodgkin-Huxley model for nerve impulse. Mechanical models have been proposed. This note reviews the experimental properties of the nerve impulse and discusses the proposed alternatives.

Comment on "Dynamically induced heat rectification in quantum systems".

The article by Riera-Campeny, Mehboudi, Pons, and Sanpera [Phys. Rev. E 99, 032126 (2019)2470-004510.

Melting Transition of Oriented DNA Fibers Submerged in Poly(ethylene glycol) Solutions Studied by Neutron Scattering and Calorimetry.

The influence of molecular confinement on the melting transition of oriented Na-DNA fibers submerged in poly(ethylene glycol) (PEG) solutions has been studied. The PEG solution exerts an osmotic pressure on the fibers which, in turn, is related to the DNA intermolecular distance. Calorimetry measurements show that the melting temperature increases and the width of the transition decreases with decreasing intermolecular distance.

Melting of highly oriented fiber DNA subjected to osmotic pressure.

A pilot study of the possibility to investigate temperature-dependent neutron scattering from fiber-DNA in solution is presented. The study aims to establish the feasibility of experiments to probe the influence of spatial confinement on the structural correlation and the formation of denatured bubbles in DNA during the melting transition. Calorimetry and neutron scattering experiments on fiber samples immersed in solutions of poly(ethylene glycol) (PEG) prove that the melting transition occurs in these samples, that the transition is reversible to some degree, and that the transition is broader in temperature than for humidified fiber samples.

Ionic mobility in DNA films studied by dielectric spectroscopy.

Double-helix DNA molecules can be found under different conformational structures driven by ionic and hydration surroundings. Usually, only the B-form of DNA, which is the only form stable in aqueous solution, can be studied by dielectric measurements. Here, the dielectric responses of DNA molecules in the A- and B-form, oriented co-linearly within fibres assembled in a film have been analyzed.

Characterization of the low-temperature properties of a simplified protein model.

Prompted by results that showed that a simple protein model, the frustrated Gō model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature properties of proteins. First, we examine equilibrium fluctuations. We calculate its incoherent neutron-scattering structure factor and show that it can be well described by a theory using the one-phonon approximation.

Temperature dependence of the DNA double helix at the nanoscale: structure, elasticity, and fluctuations.

Biological organisms exist over a broad temperature range of -15°C to +120°C, where many molecular processes involving DNA depend on the nanoscale properties of the double helix. Here, we present results of extensive molecular dynamics simulations of DNA oligomers at different temperatures. We show that internal basepair conformations are strongly temperature-dependent, particularly in the stretch and opening degrees of freedom whose harmonic fluctuations can be considered the initial steps of the DNA melting pathway.

Purification of A-form DNA fiber samples by the removal of B-form DNA residues.

To date, fiber diffraction on A-form NaDNA has always shown a B-form contamination. Here we have used optic microscopy, calorimetry, and neutron scattering techniques to define a method to obtain DNA fibres samples whose molecules are purely in the A-form. When the impure sample is heated to 320 K, the DNA molecules in the B-form undergo a transition into the A-form.

Glassy behavior of denatured DNA films studied by differential scanning calorimetry.

We use differential scanning calorimetry (DSC) to study the properties of DNA films, made of oriented fibers, heated above the thermal denaturation temperature of the double helical form. The films show glassy properties that we investigate in two series of experiments, a slow cooling at different rates followed by a DSC scan upon heating and aging at a temperature below the glass transition. Introducing the fictive temperature to characterize the glass allows us to derive quantitative information on the relaxations of the DNA films, in particular to evaluate their enthalpy barrier.

Base pair openings and temperature dependence of DNA flexibility.

The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot model with soft and hard joints, corresponding to open and closed base pairs, and sequence-dependent statistical information about the state of each pair provided by a Peyrard-Bishop-Dauxois (PBD) model calculation with no freely adjustable parameters.

Structural correlations and melting of B-DNA fibers.

Despite numerous attempts, understanding the thermal denaturation of DNA is still a challenge due to the lack of structural data on the transition since standard experimental approaches to DNA melting are made in solution and do not provide spatial information. We report a measurement using neutron scattering from oriented DNA fibers to determine the size of the regions that stay in the double-helix conformation as the melting temperature is approached from below. A Bragg peak from the B form of DNA is observed as a function of temperature and its width and integrated intensity are measured.

Thermal denaturation of DNA studied with neutron scattering.

The melting transition of DNA, whereby the strands of the double-helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fiber DNA has been measured as a function of temperature, and its widths and integrated intensities have been interpreted using the Peyrard-Bishop-Dauxois model with only one free parameter. The experiment is unique, as it gives spatial correlation along the molecule through the melting transition where other techniques cannot.

Guanine radical chemistry reveals the effect of thermal fluctuations in gene promoter regions.

DNA is not the static entity that structural pictures suggest. It has been longly known that it 'breathes' and fluctuates by local opening of the bases. Here we show that the effect of structural fluctuations, exhibited by AT-rich low stability regions present in some common transcription initiation regions, influences the properties of DNA in a distant range of at least 10 bp.

Critical examination of the inherent-structure-landscape analysis of two-state folding proteins.

Recent studies attracted the attention on the inherent-structure-landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single topology of a two-state folding protein, and the simplifying assumptions of the method have not been examined. In this work, we construct the thermodynamics of four two-state folding proteins of different sizes and secondary structure by molecular dynamics (MD) simulations using the ISL method and critically examine possible limitations of the method.

Modeling protein thermodynamics and fluctuations at the mesoscale.

We use an extended Go model, in unfrustrated and frustrated variants, to study the energy landscape and the fluctuations of a model protein. The model exhibits two transitions, folding and dynamical transitions, when changing the temperature. The inherent structures corresponding to the minima of the landscape are analyzed and we show how their energy density can be obtained from simulations around the folding temperature.

The inherent structure landscape of a protein.

Using the Gō model of a real protein, we explore the landscape of its metastable structures. First, we show how the inherent structure energy density can be obtained from the probability density determined by sampling molecular dynamics trajectories and quenching. The analysis of the inherent structure landscape can characterize the folding transition.

Can one predict DNA transcription start sites by studying bubbles?

It has been speculated that bubble formation of several base pairs due to thermal fluctuations is indicatory for biologically active sites. Recent evidence, based on experiments and molecular dynamics simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom, which makes an accurate calculation difficult even for minimal models.

A model on the origin of RNA.

The theory of the liquid-glass transition is extended to describe the polymerization of RNA in a nucleotide-condensed state. In the glassy state the ribose subunits are joined by a 2'-5' or 3'-5' phosphodiester linkage to form the ribose-phosphate backbone similar to oligosaccharides and polysaccharides. The occurrence of the glass transition requires two conditions: (1) a supercooled state in a nucleotide-condensed state should exist below the temperature at which the whole RNA hydrolyzes; (2) the Gibbs free energy due to the Kauzmann entropy, which obeys a Curie law with a negative sign, must be larger than the height of the potential barrier for nucleotides to overcome to form the binding.

Nonlinear structures and thermodynamic instabilities in a one-dimensional lattice system.

The equilibrium states of the discrete Peyrard-Bishop Hamiltonian with one end fixed are computed exactly from the two-dimensional nonlinear Morse map. These exact nonlinear structures are interpreted as domain walls, interpolating between bound and unbound segments of the chain. Their free energy is calculated to leading order beyond the Gaussian approximation.

Thermal denaturation of a helicoidal DNA model.

We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e., the separation of the two strands upon heating.

One-dimensional "turbulence" in a discrete lattice.

We study a one-dimensional discrete analog of the von Karman flow, widely investigated in turbulence. A lattice of anharmonic oscillators is excited by both ends in order to create a large scale structure in a highly nonlinear medium, in the presence of a dissipative term proportional to the second order finite difference of the velocities, similar to the viscous term in a fluid. In a first part, the energy density is investigated in real and Fourier space in order to characterize the behavior of the system on a local scale.