RESUMEN
We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulations. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which agrees with the previous predictions of circular DNA melting in the presence of supercoiling. By analyzing sector-wise changes in average base-pair distance, our study reveals that the melting behavior of circular DNA closely resembles that of linear DNA. Additionally, we find a marked difference in the thermal stability of circular DNA over linear DNA at very short length scales, an effect that diminishes as the length of circular DNA increases. The stability of smaller circular DNA is linked to the occurrence of transient small bubbles, characterized by a lower probability of growth.
Asunto(s)
ADN Circular , Desnaturalización de Ácido Nucleico , ADN Circular/química , Conformación de Ácido Nucleico , Simulación de Dinámica Molecular , Temperatura de Transición , ADN/química , TermodinámicaRESUMEN
We determine the phase diagram of DNA with inter- and intrastrand native-pair interactions that mimic the compaction of DNA. We show that DNA takes an overall sheetlike structure in the region where an incipient transition to a compact phase would have occurred. The stability of this phase is due to the extra entropy from the folding of the sheet, which is absent in the remaining polymerlike states of the phase diagram.
Asunto(s)
Pliegue de Proteína , Entropía , TermodinámicaRESUMEN
Social insects have evolved a variety of architectural formations. Bees and wasps are well known for their ability to achieve compact structures by building hexagonal cells. Polistes wattii, an open nesting paper wasp species, builds planar hexagonal structures. Here, using the pair correlation function approach, we show that their nests exhibit short-range hexagonal order (no long-range order) akin to amorphous materials. Hexagonal orientational order was well preserved globally. We also show the presence of topological defects such as dislocations (pentagon-heptagon disclination pairs) and Stone-Wales quadrupoles, and discuss how these defects were organised in the nest, thereby restoring order. Furthermore, we suggest the possible role of such defects in shaping nesting architectures of other social insect species.
Asunto(s)
Avispas , Animales , Abejas , Comportamiento de Nidificación , Conducta SocialRESUMEN
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.
Asunto(s)
ADN/química , Modelos Moleculares , Conformación de Ácido Nucleico , Transición de FaseRESUMEN
Near the melting transition the bending elastic constant κ, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rodlike scaling for small-length N. The reduction in κ with temperature is determined by the denatured bubbles for a continuous transition, e.g., when the two strands are Gaussian, but by the broken bonds near the open end in a Y-like configuration for a first-order transition as for strands with excluded volume interactions. In the latter case, a lever rule is operational, implying a phase coexistence although dsDNA is known to be a single phase.
Asunto(s)
ADN/química , Fenómenos Mecánicos , Fenómenos Biomecánicos , Modelos Moleculares , Conformación de Ácido Nucleico , Desnaturalización de Ácido Nucleico , Temperatura de TransiciónRESUMEN
We show that dynamic quantum phase transitions (DQPT) in many situations involve renormalization group (RG) fixed points that are unphysical in the context of thermal phase transitions. In such cases, boundary conditions are shown to become relevant to the extent of even completely suppressing the bulk transitions. We establish these by performing an exact RG analysis of the quantum Ising model on scale-invariant lattices of different dimensions, and by analyzing the zeros of the Loschmidt amplitude. Further corroboration of boundaries affecting the bulk transition comes from the three-state quantum Potts chain, for which we also show that the DQPT corresponds to a pair of period-2 fixed points.
RESUMEN
The totally asymmetric simple exclusion process along with particle adsorption and evaporation kinetics is a model of boundary-induced nonequilibrium phase transition. In the continuum limit, the average particle density across the system is described by a singular differential equation involving multiple scales which lead to the formation of boundary layers (BL) or shocks. A renormalization group analysis is developed here by using the location and the width of the BL as the renormalization parameters. It not only allows us to cure the large distance divergences in the perturbative solution for the BL but also generates, from the BL solution, an analytical form for the global density profile. The predicted scaling form is checked against numerical solutions for finite systems.
RESUMEN
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in the other the double-stranded DNA is taken to have an intrinsic rigidity for bending. In both cases single strands are completely flexible. The change in the elastic constant for the flexible case due to thermally generated bubbles is obtained exactly. For the case of intrinsic rigidity, the elastic constant is found to be proportional to the square root of the bubble number fluctuation.
Asunto(s)
ADN/química , Elasticidad , Fenómenos Biomecánicos , Modelos Moleculares , Conformación de Ácido Nucleico , Desnaturalización de Ácido Nucleico , Termodinámica , Temperatura de TransiciónRESUMEN
A three-stranded DNA with short range base pairings only is known to exhibit a classical analog of the quantum Efimov effect, viz., a three-chain bound state at the two-chain melting point where no two are bound. By using a nonperturbative renormalization-group method for a rigid duplex DNA and a flexible third strand, with base pairings and strand exchange, we show that the Efimov-DNA is associated with a limit cycle type behavior of the flow of an effective three-chain interaction. The analysis also shows that thermally generated bubbles play an essential role in producing the effect. A toy model for the flow equations shows the limit cycle in an extended three-dimensional parameter space of the two-chain coupling and a complex three-chain interaction.
Asunto(s)
ADN/química , Modelos Químicos , Modelos Genéticos , Conformación de Ácido Nucleico , Polímeros/química , Temperatura de TransiciónRESUMEN
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and Scheraga models). Within this framework, the existence of a three-stranded DNA bound state in conditions where a duplex DNA would be in the denaturated state was recently predicted from a study of three directed polymer models on simplified hierarchical lattices (d>2) and in 1+1 dimensions. Such a phenomenon which is similar to the Efimov effect in nuclear physics was named Efimov-DNA. In this paper we study the melting of the three-stranded DNA on a Sierpinski gasket of dimensions d<2 by assigning extra weight factors to fork openings and closings, to induce a two-strand DNA melting. In such a context we can find again the existence of the Efimov-DNA-like state but quite surprisingly we discover also the presence of a different phase, to be called a mixed state, where the strands are pair-wise bound but without three chain contacts. Whereas the Efimov DNA turns out to be a crossover near melting, the mixed phase is a thermodynamic phase.
Asunto(s)
ADN/química , ADN/ultraestructura , Modelos Químicos , Modelos Moleculares , Temperatura de Transición , Secuencia de Bases , Simulación por Computador , Datos de Secuencia Molecular , Conformación de Ácido Nucleico , Desnaturalización de Ácido Nucleico , Transición de Fase , TemperaturaRESUMEN
We review various simple analytical theories for homopolymers within a unified framework. The common guideline of our approach is the Flory theory, and its various avatars, with the attempt at being reasonably self-contained. We expect this review to be useful as an introduction to the topic at the graduate student level.
Asunto(s)
Polímeros/química , Teoría Cuántica , Modelos Químicos , TermodinámicaRESUMEN
Replication and transcription are two important processes in living systems. To execute such processes, various proteins work far away from equilibrium in a staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA under a periodic drive are studied. A steady-state phase diagram of a driven DNA is proposed which is experimentally verifiable. As a two-state system, we also compare the results of DNA with that of an Ising magnet under an asymmetrical variation of the magnetic field.
Asunto(s)
ADN/química , ADN/efectos de la radiación , Modelos Químicos , Modelos Moleculares , Simulación por Computador , ADN/ultraestructura , Campos Magnéticos , Transición de Fase/efectos de la radiaciónRESUMEN
We show that there exists an Efimov-like three strand DNA bound state at the duplex melting point and it is described by a renormalization group limit cycle. A nonperturbative renormalization group is used to obtain this result in a model involving short range pairing only. Our results suggest that Efimov physics can be tested in polymeric systems.
Asunto(s)
ADN/química , Modelos Químicos , Conformación de Ácido Nucleico , Temperatura de TransiciónRESUMEN
We study the melting of three-stranded DNA by using the real-space renormalization group and exact recursion relations. The prediction of an unusual Efimov-analog three-chain bound state, that appears at the critical melting of two-chain DNA, is corroborated by the zeros of the partition function. The distribution of the zeros has been studied in detail for various situations. We show that the Efimov DNA can occur even if the three-chain (i.e., three-monomer) interaction is repulsive in nature. In higher dimensions, a striking result that emerged in this repulsive zone is a continuous transition from the critical state to the Efimov DNA.
Asunto(s)
Biofisica/métodos , ADN/química , Conformación de Ácido Nucleico , Algoritmos , Simulación por Computador , ADN/genética , Expresión Génica , Perfilación de la Expresión Génica , Modelos Químicos , Modelos Estadísticos , Modelos Teóricos , Biología Molecular , Conformación Molecular , Distribución Normal , Polímeros/químicaRESUMEN
A repair protein like RecG moves the stalled replication fork in the direction from the zipped to the unzipped state of DNA. It is proposed here that a softening of the zipped-unzipped interface at the fork results in the front propagating towards the unzipped side. In this scenario, an ordinary helicase destabilizes the zipped state locally near the interface and the fork propagates towards the zipped side. The softening of the interface can be produced by the aromatic interaction, predicted from the crystal structure, between RecG and the nascent broken base pairs at the Y-fork. A numerical analysis of the model also reveals the possibility of a stop and go type motion.
Asunto(s)
Reparación del ADN , ADN/química , Proteínas de Escherichia coli/química , Algoritmos , Biofisica/métodos , Cristalización , Replicación del ADN , Escherichia coli/metabolismo , Modelos Estadísticos , Modelos Teóricos , Conformación de Ácido Nucleico , Factores de TiempoRESUMEN
We study the effect of random forces on a double-stranded DNA in unzipping the two strands, analogous to the problem of an adsorbed polymer under a random force. The ground state develops bubbles of various lengths as the random force fluctuation is increased. The unzipping phase diagram is shown to be drastically different from the pure case.
Asunto(s)
ADN/química , Conformación de Ácido Nucleico , Desnaturalización de Ácido Nucleico , Fenómenos Biofísicos , Biofisica , Modelos Químicos , TermodinámicaRESUMEN
The phase diagram of unzipping of an adsorbed directed polymer in two dimensions in a random medium has been determined. Both the hard-wall and the soft-wall cases are considered. Exact solutions for the pure problem with different affinities on the two sides are given. The results obtained by the numerical procedure adopted here are shown to agree with the exact results for the pure case. The characteristic exponents for unzipping for the random problem are different from the pure case. The distribution functions for the unzipped length, first bubble, and the spacer are determined.
RESUMEN
We show the existence of a force induced triple point in an interacting polymer problem that allows two zero-force thermal phase transitions. The phase diagrams for two different models of mutually attracting but self-avoiding polymers are presented. One of these models has an intermediate phase and it shows a triple point. A general phase diagram with multicritical points in an extended parameter space is also discussed.
RESUMEN
We study the unzipping of double stranded DNA by applying a pulling force at a fraction s (0< or =s < or =1) from the anchored end. From exact analytical and numerical results, the complete phase diagram is presented. The phase diagram shows a strong ensemble dependence for various values of s. In addition, we show the existence of an eye phase and a triple point.
Asunto(s)
ADN/química , Modelos Biológicos , ADN/metabolismo , Conformación de Ácido Nucleico , TermodinámicaRESUMEN
We report studies of the dynamics of a set of exactly solvable lattice models for the force-induced DNA unzipping transition. Besides yielding the whole equilibrium phase diagram, which reveals a reentrance, these models enable us to characterize the dynamics of the process starting from a nonequilibrium initial condition. The thermal melting of DNA displays a model dependent time evolution. On the contrary, the dynamical mechanism for the unzipping by force is very robust and the scaling behavior is independent of the details of the description and, hence, superuniversal.