The Order of Phase Transition of Solvable DNA Melting Models

2003 ◽  
Vol 17 (16) ◽  
pp. 885-896 ◽  
Author(s):  
Su-Long Nyeo ◽  
I-Ching Yang
Keyword(s):  
Phase Transition ◽  
Hydrogen Bonds ◽  
Short Range ◽  
Scaling Laws ◽  
Dna Melting ◽  
Thermodynamic Quantities ◽  
Base Pairs ◽  
Order Of Phase Transition ◽  
Exactly Solvable ◽  
Dna Models

The phase transition of DNA molecules is studied in an exactly solvable formalism with the Morse and Deng–Fan potentials for the interstrand hydrogen bonds of nucleotide base pairs. It is shown that although the two potentials have different short-range behaviors, the thermodynamic quantities of the DNA system in these potentials enjoy the same scaling laws with the associated critical exponents, which are explicitly calculated. These exactly solvable DNA models are shown to exhibit a phase transition of the second order and the results of the analysis agree with previous studies.

PHASE TRANSITION, GEOMETROTHERMODYNAMICS AND CRITICAL EXPONENTS OF BARDEEN BLACK HOLE

2014 ◽  
Vol 23 (04) ◽  
pp. 1450040
Author(s):  
JIE-XIONG MO
Keyword(s):  
Phase Transition ◽  
Black Hole ◽  
Specific Heat ◽  
Critical Exponents ◽  
Transition Point ◽  
Scaling Laws ◽  
Phase Transition Point ◽  
Invariant Metrics ◽  
Thermodynamic Quantities ◽  
Transition Structure

In this paper, we investigate the phase transition of Bardeen black hole for the first time. First, we calculate thermodynamic quantities and correct the misuse of formula in former literature. Second, we investigate in detail the behavior of specific heat. We not only discuss the influence of parameter on phase transition, but also show the three-dimensional behavior of the specific heat. It is shown that phase transition takes place from a locally unstable large black hole to a locally stable small black hole. It is also shown that the location of phase transition point is proportional to the charge. Meanwhile, we study the behavior of the inverse of the isothermal compressibility and find that it diverges at the phase transition point. Thirdly, we build up geometrothermodynamics to examine the phase transition structure. It is shown that Legendre invariant thermodynamic scalar curvature diverges exactly where the specific heat diverges, which leads to the conclusion that the Legendre invariant metrics can correctly produce the behavior of the phase transition structure. Furthermore, to gain a thorough understanding of critical behavior, we calculate the relevant critical exponents and examine the scaling laws. It is shown that they are in agreement with the scaling laws.

scholarly journals Gluodynamics and deconfinement phase transition under rotation from holography

2021 ◽  
Vol 2021 (7) ◽  
Author(s):  
Xun Chen ◽  
Lin Zhang ◽  
Danning Li ◽  
Defu Hou ◽  
Mei Huang
Keyword(s):  
Phase Transition ◽  
Angular Velocity ◽  
Chemical Potential ◽  
Entropy Density ◽  
Thermodynamic Quantities ◽  
Strongly Coupled ◽  
Trace Anomaly ◽  
Holographic Qcd ◽  
Deconfinement Phase Transition ◽  
Small Chemical

Abstract We investigate rotating effect on deconfinement phase transition in an Einstein-Maxwell-Dilaton (EMD) model in bottom-up holographic QCD approach. By constructing a rotating black hole, which is supposed to be dual to rotating strongly coupled nuclear matter, we investigate the thermodynamic quantities, including entropy density, pressure, energy density, trace anomaly, sound speed and specific heat for both pure gluon system and two-flavor system under rotation. It is shown that those thermodynamic quantities would be enhanced by large angular velocity. Also, we extract the information of phase transition from those thermodynamic quantities, as well as the order parameter of deconfinement phase transition, i.e. the loop operators. It is shown that, in the T − ω plane, for two-flavor case with small chemical potential, the phase transition is always crossover. The transition temperature decreases slowly with angular velocity and chemical potential. For pure gluon system with zero chemical potential, the phase transition is always first order, while at finite chemical potential a critical end point (CEP) will present in the T − ω plane.

Finding Short-Range Parity-Time Phase-Transition Points with a Neural Network

2021 ◽  
Vol 38 (5) ◽  
pp. 051101
Author(s):  
Songju Lei ◽  
Dong Bai ◽  
Zhongzhou Ren ◽  
Mengjiao Lyu
Keyword(s):  
Neural Network ◽  
Phase Transition ◽  
Short Range ◽  
Transition Points

Cooperative vibrational properties of hydrogen bonds in Watson–Crick DNA base pairs

2017 ◽  
Vol 41 (20) ◽  
pp. 12104-12109 ◽  
Author(s):  
Yulei Shi ◽  
Wanrun Jiang ◽  
Zhiyuan Zhang ◽  
Zhigang Wang
Keyword(s):  
Hydrogen Bonds ◽  
Vibrational Properties ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs

For the AT pair, Symst and Strech peaks further shift toward the red, giving the H-bonds an amplified effect (orange arrows).

scholarly journals Scaling laws describe memories of host–pathogen riposte in the HIV population

2015 ◽  
Vol 112 (7) ◽  
pp. 1965-1970 ◽  
Author(s):  
John P. Barton ◽  
Mehran Kardar ◽  
Arup K. Chakraborty
Keyword(s):  
Neural Networks ◽  
Immune Responses ◽  
Scaling Laws ◽  
Mechanistic Model ◽  
Solvable Model ◽  
Effective Control ◽  
Immune Selection ◽  
Exactly Solvable ◽  
Host Pathogen ◽  
Human Immune

The enormous genetic diversity and mutability of HIV has prevented effective control of this virus by natural immune responses or vaccination. Evolution of the circulating HIV population has thus occurred in response to diverse, ultimately ineffective, immune selection pressures that randomly change from host to host. We show that the interplay between the diversity of human immune responses and the ways that HIV mutates to evade them results in distinct sets of sequences defined by similar collectively coupled mutations. Scaling laws that relate these sets of sequences resemble those observed in linguistics and other branches of inquiry, and dynamics reminiscent of neural networks are observed. Like neural networks that store memories of past stimulation, the circulating HIV population stores memories of host–pathogen combat won by the virus. We describe an exactly solvable model that captures the main qualitative features of the sets of sequences and a simple mechanistic model for the origin of the observed scaling laws. Our results define collective mutational pathways used by HIV to evade human immune responses, which could guide vaccine design.

Three-centre C—H...O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures

1999 ◽  
Vol 55 (12) ◽  
pp. 2005-2012 ◽  
Author(s):  
Anirban Ghosh ◽  
Manju Bansal
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Base Pair ◽  
Minor Groove ◽  
Local Geometry ◽  
Data Sets ◽  
Base Pairs ◽  
Dna Minor Groove ◽  
Close Proximity ◽  
Using Data

AA·TT and GA·TC dinucleotide steps in B-DNA-type oligomeric crystal structures and in protein-bound DNA fragments (solved using data with resolution <2.6 Å) show very small variations in their local dinucleotide geometries. A detailed analysis of these crystal structures reveals that in AA·TT and GA·TC steps the electropositive C2—H2 group of adenine is in very close proximity to the keto O atoms of both the pyrimidine bases in the antiparallel strand of the duplex structure, suggesting the possibility of intra-base pair as well as cross-strand inter-base pair C—H...O hydrogen bonds in the DNA minor groove. The C2—H2...O2 hydrogen bonds in the A·T base pairs could be a natural consequence of Watson–Crick pairing. However, the cross-strand interactions between the bases at the 3′-end of the AA·TT and GA·TC steps obviously arise owing to specific local geometry of these steps, since a majority of the H2...O2 distances in both data sets are considerably shorter than their values in the uniform fibre model (3.3 Å) and many are even smaller than the sum of the van der Waals radii. The analysis suggests that in addition to already documented features such as the large propeller twist of A·T base pairs and the hydration of the minor groove, these C2—H2...O2 cross-strand interactions may also play a role in the narrowing of the minor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA)·poly(dT).

Structure of ammonium hydrogen succinate above and below the phase transition around 170K

1996 ◽  
Vol 52 (2) ◽  
pp. 323-327 ◽  
Author(s):  
A. Hirano ◽  
Y. Kubozono ◽  
H. Maeda ◽  
H. Ishida ◽  
S. Kashino
Keyword(s):  
Crystal Structure ◽  
Phase Transition ◽  
Hydrogen Bonds ◽  
Order Phase Transition ◽  
Space Group ◽  
X Ray ◽  
Ammonium Hydrogen ◽  
Significant Change ◽  
Short Hydrogen Bonds ◽  
Second Order Phase Transition

For crystals of ammonium hydrogen succinate it is known that the space group is P{\bar 1} with Z = 2 at 293 K and the second-order phase transition occurs around 170 K. X-ray crystal structure analyses above and below 170 K have been carried out in order to study the change in mode of short hydrogen bonds between the hydrogen succinate ions. The space group was determined to be P{\bar 1} at 150 and 190 K by structure analysis. No ordering of the H-atom positions in the short hydrogen bonds occurs by the phase transition. The hydrogen bonds show a decrease in the O...O distances with a decrease in temperature from 290 to 190 K, but no significant change in the geometries between 190 and 150 K. Disorder of the NH4 + ion is not observed at 297, 190 and 150 K. Significant change through the phase transition is found only in the geometry of one of the N—H...O hydrogen bonds between ammonium and hydrogen succinate ions.

scholarly journals Phase diagram of the selfinteracting particle­-antiparticle boson system

2021 ◽  
Vol 29 (1) ◽  
pp. 5-14
Author(s):  
D. Anchishkin ◽  
V. Gnatovskyy ◽  
D. Zhuravel ◽  
V. Karpenko
Keyword(s):  
Phase Transition ◽  
Phase Diagram ◽  
Phase Diagrams ◽  
Canonical Ensemble ◽  
Bose Condensate ◽  
Mean Field ◽  
Thermodynamic Quantities ◽  
Boson System ◽  
The Mean

A system of interacting relativistic bosons at finite temperatures and isospin densities is studied within the framework of the Skyrme­like mean­field model. The mean field contains both attractive and repulsive terms. The consideration is taken within the framework of the Canonical Ensemble and the isospin­density dependencies of thermodynamic quantities is obtained, in particular as the phase diagrams. It is shown that in such a system, in addition to the formation of a Bose­Einstein condensate, a liquid­gas phase transition is possible. We prove that the multi­boson system develops the Bose condensate for particles of high­density component only.

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