Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Thermodynamics of freezing and melting.

ABSTRACT: Although the freezing of liquids and melting of crystals are fundamental for many areas of the sciences, even simple properties like the temperature-pressure relation along the melting line cannot be predicted today. Here we present a theory in which properties of the coexisting crystal and liquid phases at a single thermodynamic state point provide the basis for calculating the pressure, density and entropy of fusion as functions of temperature along the melting line, as well as the variation along this line of the reduced crystalline vibrational mean-square displacement (the Lindemann ratio), and the liquid's diffusion constant and viscosity. The framework developed, which applies for the sizable class of systems characterized by hidden scale invariance, is validated by computer simulations of the standard 12-6 Lennard-Jones system.

SUBMITTER: Pedersen UR

PROVIDER: S-EPMC4992064 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Thermodynamics of freezing and melting.

Pedersen Ulf R UR Costigliola Lorenzo L Bailey Nicholas P NP Schrøder Thomas B TB Dyre Jeppe C JC

Nature communications 20160817

Although the freezing of liquids and melting of crystals are fundamental for many areas of the sciences, even simple properties like the temperature-pressure relation along the melting line cannot be predicted today. Here we present a theory in which properties of the coexisting crystal and liquid phases at a single thermodynamic state point provide the basis for calculating the pressure, density and entropy of fusion as functions of temperature along the melting line, as well as the variation a ...[more]

PMID: 27530064

Similar Datasets

Melting thermodynamics of reversible DNA/ligand complexes at interfaces.

Project description:A variety of solution methods exist for analysis of interactions between small molecule ligands and nucleic acids; however, accomplishing this task economically at the scale of hundreds to thousands of sequences remains challenging. Surface assays offer a prospective solution through array-based multiplexing, capable of mapping out the full sequence context of a DNA/ligand interaction in a single experiment. However, relative to solution assays, accurate quantification of DNA/ligand interactions in a surface format must contend with limited understanding of molecular activities and interactions at a solid-liquid interface. We report a surface adaptation of a solution method in which shifts in duplex stability, induced by ligand binding and quantified from melting transitions, are used for thermodynamic analysis of DNA/ligand interactions. The results are benchmarked against solution calorimetric data. Equilibrium operation is confirmed through superposition of denaturation/hybridization transitions triggered by heating and cooling. The antibiotic compound netropsin, which undergoes electrostatic and sequence-specific minor groove interactions with DNA, is used as a prototypical small molecule. DNA/netropsin interactions are investigated as a function of ionic strength and drug concentration through electrochemical tracing of surface melt transitions. Comparison with solution values finds excellent agreement in free energy, though reliable separation into enthalpic and entropic contributions proves more difficult. The results establish key guidelines for analysis of DNA-ligand interactions via reversible melting denaturation at surfaces.

| S-EPMC3498581 | biostudies-literature

A sudden-melting event during water freezing inside a copper well.

Project description:We studied the freezing of super-cooled water inside a millimeter-sized copper well by confocal microscopy. During freezing, we surprisingly observed a novel melting scenario, which we call a 'sudden-melting event': the ice directly above the bottom substrate suddenly melts in the late stage of the freezing process, while the system is continuously being cooled. After this event, an empty gap around 10 μm to 20 μm between the substrate and the bulk ice is formed. Because this gap occupies the majority of the area of the bottom substrate, the adhesion between the bulk ice and the substrate is greatly reduced: the adhesion force decreases by more than 50% compared with the flat-substrate situation. We further discovered that air dissolved in water plays a crucial role in this melting event: the air excluded by water freezing produces inter-connecting channels in the bulk ice, which transport the warm water produced by latent heat to the substrate which causes the sudden melting event. Because this event makes the contact between ice and substrate very poor, and greatly reduces ice adhesion, our observation may lead to a promising anti-icing method on solid substrates. Compared to the prevalent super-hydrophobic surface technique, our approach only requires millimeter-sized wells instead of complex microscopic textures. Therefore, it is much easier and cheaper to produce, as well as much more robust for large-scale practical applications.

| S-EPMC9088081 | biostudies-literature

The influence of Pseudomonas syringae on water freezing and ice melting.

Project description:Pseudomonas syringae is a widely spread plant pathogen known to have ice-nucleating proteins that serve as crystallization sites promoting ice growth at near-zero temperatures. Three temperatures that characterize water freezing and ice melting are (i) the freezing point of water, (ii) the temperature of coexistence of ice and water, and (iii) the melting point of ice. Here we show the influence of different concentrations of P. syringae on these three parameters. P. syringae appears to affect both the freezing point of water and the temperature of the coexistence of ice and water. Additionally, we propose a research technique for studying the freezing/melting process that is simple and requires no complex equipment.

| S-EPMC9098023 | biostudies-literature

In situ study on atomic mechanism of melting and freezing of single bismuth nanoparticles.

Project description:Experimental study of the atomic mechanism in melting and freezing processes remains a formidable challenge. We report herein on a unique material system that allows for in situ growth of bismuth nanoparticles from the precursor compound SrBi2Ta2O9 under an electron beam within a high-resolution transmission electron microscope (HRTEM). Simultaneously, the melting and freezing processes within the nanoparticles are triggered and imaged in real time by the HRTEM. The images show atomic-scale evidence for point defect induced melting, and a freezing mechanism mediated by crystallization of an intermediate ordered liquid. During the melting and freezing, the formation of nucleation precursors, nucleation and growth, and the relaxation of the system, are directly observed. Based on these observations, an interaction-relaxation model is developed towards understanding the microscopic mechanism of the phase transitions, highlighting the importance of cooperative multiscale processes.

| S-EPMC5316836 | biostudies-literature

Can Halophilic and Psychrophilic Microorganisms Modify the Freezing/Melting Curve of Cold Salty Solutions? Implications for Mars Habitability.

Project description:We present the hypothesis that microorganisms can change the freezing/melting curve of cold salty solutions by protein expression, as it is known that proteins can affect the liquid-to-ice transition, an ability that could be of ecological advantage for organisms on Earth and on Mars. We tested our hypothesis by identifying a suitable candidate, the well-known psycrophile and halotolerant bacteria Rhodococcus sp. JG3, and analyzing its response in culture conditions that included specific hygroscopic salts relevant to Mars-that is, highly concentrated magnesium perchlorate solutions of 20 wt % and 50 wt % Mg(ClO4)2 at both end members of the eutectic concentration (44 wt %)-and subfreezing temperatures (263 K and 253 K). Using a combination of techniques of molecular microbiology and aqueous geochemistry, we evaluated the potential roles of proteins over- or underexpressed as important players in different mechanisms for the adaptability of life to cold environments. We recorded the changes observed by micro-differential scanning calorimetry. Unfortunately, Rhodococcus sp. JG3 did not show our hypothesized effect on the melting characteristics of cold Mg-perchlorate solutions. However, the question remains as to whether our novel hypothesis that halophilic/psychrophilic bacteria or archaea can alter the freezing/melting curve of salt solutions could be validated. The null result obtained after analyzing just one case lays the foundation to continue the search for proteins produced by microorganisms that thrive in very cold, high-saline solutions, which would involve testing different microorganisms with different salt components. The immediate implications for the habitability of Mars are discussed.

| S-EPMC7116095 | biostudies-literature

Melting the EIS

Project description:Melting the Eis: non-detection of kanamycin resistance markers by routine diagnostic tests and identification of new eis-promoter variants

| PRJEB41458 | ENA

Effect of Type I Antifreeze Proteins on the Freezing and Melting Processes of Cryoprotective Solutions Studied by Site-Directed Spin Labeling Technique.

Project description:Antifreeze proteins (AFPs) protect organisms living in subzero environments from freezing injury, which render them potential applications for cryopreservation of living cells, organs, and tissues. Cryoprotective agents (CPAs), such as glycerol and propylene glycol, have been used as ingredients to treat cellular tissues and organs to prevent ice crystal's formation at low temperatures. To assess AFP's function in CPA solutions, we have the applied site-directed spin labeling technique to a Type I AFP. A two-step process to prevent bulk freezing of the CPA solutions was observed by the cryo-photo microscopy, i.e., (1) thermodynamic freezing point depression by the CPAs; and (2) inhibition to the growth of seed ice crystals by the AFP. Electron paramagnetic resonance (EPR) experiments were also carried out from room temperature to 97 K, and vice versa. The EPR results indicate that the spin labeled AFP bound to ice surfaces, and inhibit the growths of ice through the bulk freezing processes in the CPA solutions. The ice-surface bound AFP in the frozen matrices could also prevent the formation of large ice crystals during the melting processes of the solutions. Our study illustrates that AFPs can play an active role in CPA solutions for cryopreservation applications.

| S-EPMC7678753 | biostudies-literature

Recovery from freezing

Project description:Screening of genes that respond to cryopreservation stress using yeast DNA microarray.: We studied the response of yeast cells after cryopreservation treatment using DNA microarray technology. Genes that contribute to "Cell rescue, defense and virulence," "energy," and "metabolism," were significantly induced. These genes were classified as encoding heat shock proteins, oxidative stress scavenger, and enzymes involved in glucose metabolism. The expression profile of mRNA after cryopreservation treatment was calculated to be closer to that following treatment with detergent or plant oils rather than by other stress factors such as heavy metals and agricultural chemicals. These results suggest that the cryopreservation treatment caused damage to the structure of the cell wall and cellular organelles. This was supported by the localization of the products of the induced genes at the cell wall and within cellular organelles. Keywords: stress response

2007-11-01 | GSE9404 | GEO

Thermodynamics Beyond Molecules: Statistical Thermodynamics of Probability Distributions

Project description:Statistical thermodynamics has a universal appeal that extends beyond molecular systems, and yet, as its tools are being transplanted to fields outside physics, the fundamental question, what is thermodynamics, has remained unanswered. We answer this question here. Generalized statistical thermodynamics is a variational calculus of probability distributions. It is independent of physical hypotheses but provides the means to incorporate our knowledge, assumptions and physical models about a stochastic processes that gives rise to the probability in question. We derive the familiar calculus of thermodynamics via a probabilistic argument that makes no reference to physics. At the heart of the theory is a space of distributions and a special functional that assigns probabilities to this space. The maximization of this functional generates the mathematical network of thermodynamic relationship. We obtain statistical mechanics as a special case and make contact with Information Theory and Bayesian inference.

| S-EPMC7515426 | biostudies-literature

Investigation of thermodynamics, and structural, dynamical, and electrical properties of polyoxometalate ionic liquid confined into carbon nanotubes during the melting process using molecular dynamics simulation.

Project description:Understanding the properties of ionic liquids confined into nano-pores is required to use ionic liquids for many applications such as electrolytes for energy storage in capacitors and solar cells. Recently, polyoxometalate ionic liquids have attracted much attention for their potential applications in electrochemistry, catalysis, and nanotechnology. In this work, we have performed MD simulations on 1-ethyl-3-methylimidazolium Keggin ([emim]3[PW12O40]) confined into armchair (20,20) CNTs to study the thermal properties and melting process. Changes in the simulated results of configurational energy of confined polyoxometallate IL indicated that the melting range of the confined polyoxometalate IL is about 650-750 K. Heat capacity at constant volume of the confined IL is about 2 (cal K-1 mol-1) which shows sharp changes around the melting range. The average number of hydrogen bonds (〈HB〉) of the confined IL is about 2.8 which also presents sharp changes around the melting range. The ion conductivity and self-diffusion coefficient of [emim]3[PW12O40] IL also present a sharp maximum of 25 (S m-1) and 6 × 10-10 (m2 s-1) at the melting point. Our results did not show a significant hysteresis in the melting process and therefore, the process is reversible. Our simulation also indicated that the confinement of the polyoxometallate IL into the CNT increases its thermal stability and melting point. Our simulations also indicated that the type of CNT configuration has a small effect on the melting point of the confined polyoxometallate IL.

| S-EPMC9782402 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data