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Journal ArticleDOI

Efimov-DNA phase diagram: Three stranded DNA on a cubic lattice.

12 Aug 2021-Journal of Chemical Physics (AIP Publishing)-Vol. 155, Iss: 6, pp 064903
TL;DR: In this article, a generalized model for three-stranded DNA consisting of two chains of one type and a third chain of a different type was defined, and the DNA strands were modeled by random walks on the three-dimensional cubic lattice with different interactions between two chains.
Abstract: We define a generalized model for three-stranded DNA consisting of two chains of one type and a third chain of a different type. The DNA strands are modeled by random walks on the three-dimensional cubic lattice with different interactions between two chains of the same type and two chains of different types. This model may be thought of as a classical analog of the quantum three-body problem. In the quantum situation, it is known that three identical quantum particles will form a triplet with an infinite tower of bound states at the point where any pair of particles would have zero binding energy. The phase diagram is mapped out, and the different phase transitions are examined using finite-size scaling. We look particularly at the scaling of the DNA model at the equivalent Efimov point for chains up to 10 000 steps in length. We find clear evidence of several bound states in the finite-size scaling. We compare these states with the expected Efimov behavior.
Citations
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Journal ArticleDOI
TL;DR: In this article , a simple coarse-grained model of DNA which includes both Watson-Crick and Hoogsteen base pairing has been used to study the melting and unzipping of triplex DNA.
Abstract: A simple coarse-grained model of DNA which includes both Watson-Crick and Hoogsteen base pairing has been used to study the melting and unzipping of triplex DNA. Using Langevin dynamics simulations, we reproduce the qualitative features of one-step and two-step thermal melting of triplex as seen in experiments. The thermal melting phase diagram shows the existence of a stable interchain three-strand complex (bubble-bound state). Our studies based on the mechanical unzipping of a triplex revealed that it is mechanically more stable compared to an isolated duplex-DNA.

2 citations

Journal ArticleDOI
01 Nov 2022-Entropy
TL;DR: In this paper , the authors summarized the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions, and provided valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.
Abstract: Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA’s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.

1 citations

References
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Journal ArticleDOI
James D. Watson1, Francis Crick1
25 Apr 1953-Nature
TL;DR: The determination in 1953 of the structure of deoxyribonucleic acid (DNA), with its two entwined helices and paired organic bases, was a tour de force in X-ray crystallography and opened the way for a deeper understanding of perhaps the most important biological process.
Abstract: The determination in 1953 of the structure of deoxyribonucleic acid (DNA), with its two entwined helices and paired organic bases, was a tour de force in X-ray crystallography. But more significantly, it also opened the way for a deeper understanding of perhaps the most important biological process. In the words of Watson and Crick: "It has not escaped our notice that the specific pairing that we have postulated immediately suggests a possible copying mechanism for the genetic material." [Obituary of Francis Crick:

9,946 citations

Journal ArticleDOI
TL;DR: In this paper, the existence of a series of levels in three-particle systems has been investigated and it has been shown that the number of such levels may be very large.

1,197 citations

Journal ArticleDOI
TL;DR: In this paper, a thorough treatment of universality for the system of three identical bosons is presented, and the universal information that is currently available for other 3-body systems is summarized.

968 citations

Journal ArticleDOI
16 Mar 2006-Nature
TL;DR: In this article, the Efimov trimer state was shown to exist in an ultracold gas of caesium atoms and its signature was observed as a giant three-body recombination loss when the strength of the two-body interaction is varied.
Abstract: In the bizarre world of quantum physics, three interacting particles can form a loosely bound system even if the two-particle attraction is too weak to allow for the binding of a pair. This exotic trimer state was predicted 35 years ago by Russian physicist Vitali Efimov, who found a remarkable and counterintuitive solution to the notoriously difficult quantum-mechanical three-body problem. Efimov's well known result was a landmark in theoretical few-body physics, but until now these exotic states had not been demonstrated experimentally. Now that has been achieved, in an ultracold gas of caesium atoms. The existence of this gas confirms key predictions and opens up few-body quantum systems to further experiment. The first experimental observation of Efimov's prediction confirms key theoretical predictions and represents a starting point from which to explore the universal properties of resonantly interacting few-body systems. Systems of three interacting particles are notorious for their complex physical behaviour. A landmark theoretical result in few-body quantum physics is Efimov's prediction1,2 of a universal set of bound trimer states appearing for three identical bosons with a resonant two-body interaction. Counterintuitively, these states even exist in the absence of a corresponding two-body bound state. Since the formulation of Efimov's problem in the context of nuclear physics 35 years ago, it has attracted great interest in many areas of physics3,4,5,6,7,8. However, the observation of Efimov quantum states has remained an elusive goal3,5. Here we report the observation of an Efimov resonance in an ultracold gas of caesium atoms. The resonance occurs in the range of large negative two-body scattering lengths, arising from the coupling of three free atoms to an Efimov trimer. Experimentally, we observe its signature as a giant three-body recombination loss9,10 when the strength of the two-body interaction is varied. We also detect a minimum9,11,12 in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point with which to explore the universal properties of resonantly interacting few-body systems7. While Feshbach resonances13,14 have provided the key to control quantum-mechanical interactions on the two-body level, Efimov resonances connect ultracold matter15 to the world of few-body quantum phenomena.

884 citations

Journal ArticleDOI
TL;DR: In this paper, a renormalization group transformation is introduced with the help of which critical properties of infinite systems can be related to finite systems, and applied to the two-dimensional Ising model.
Abstract: A renormalization group transformation is introduced with the help of which critical properties of infinite systems can be related to finite systems. As a numerical example the method is applied to the two-dimensional Ising model. The critical point and critical point exponent are computed in addition to the amplitude of the logarithmic singularity in the specific heat.

370 citations