Related papers: Partition function of a bubble formed in double st…
The different variants of two-stage random sequential adsorption (RSA) models for packing of disks and discorectangles on a two-dimensional (2D) surface were investigated. In the SD model, the discorectangles were first deposited and then…
Partition Density Functional Theory (P-DFT) is a density embedding method that partitions a molecule into fragments by minimizing the sum of fragment energies subject to a local density constraint and a global electron-number constraint. To…
We investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…
Using non-linear evolution equations of QCD, we compute the von Neumann entropy of the system of partons resolved by deep inelastic scattering at a given Bjorken $x$ and momentum transfer $q^2 = - Q^2$. We interpret the result as the…
The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions ($d\geq 5$) by using exact real space renormalization group (RG)…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
We calculate the typical bipartite entanglement entropy $\langle S_A\rangle_N$ in systems containing indistinguishable particles of any kind as a function of the total particle number $N$, the volume $V$, and the subsystem fraction…
We evaluate the two-point function for the electromagnetic field tensor in $(D+1)$-dimensional de Sitter spacetime assuming that the field is prepared in Bunch-Davies vacuum state. This two-point function is used for the investigation of…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
Bacteriophages densely pack their long dsDNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
We compute the contour integral for the partition function of an $\mathcal{N}=2$ $SU(2)$ topologically twisted theory on $\mathbb{CP}^2$, dimensionally reducing from an $\mathcal{N}=1$ theory on $S^5$. Earlier works presented the partition…
We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 < c < 1$~mM, by…
We study a family of 2d N=(0,4) gauge theories which describes at low energy the dynamics of E-strings, the M2-branes suspended between a pair of M5 and M9 branes. The gauge theory is engineered using a duality with type IIA theory, leading…
We study the basepairing dynamics of DNA with repetitive sequences where local strand slippage can create, annihilate, and move bulge loops. Using an explicit theoretical model, we find a rich dynamical behavior as a function of an applied…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
We present a theory for describing the inner structure of the electron bunch in the bubble regime starting from a random distribution of electrons inside the bubble and subsequently minimizing the system's energy. Consequently, we find a…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…