Related papers: How molecular knots can pass through each other
We show that the local parity violation in the quark-gluon plasma supports existence of free (meta)stable knots of deconfined hot quark matter stabilized by superstrong magnetic fields. The magnetic field in the knots resembles the…
In this work the thermodynamic properties of short polymer knots (up to 120 segments) defined on a simple cubic lattice are studied with the help of the Wang-Landau Monte Carlo algorithm. The sampling process is performed using pivot…
We present a very simple model for the study of charge transport in a molecule patterned on B-DNA. In this model we use a discrete non-linear Schr\"{o}dinger equation to describe electrons propagating along the sugar-phosphate backbone of…
We propose a theoretical approach to quantitatively account for the role of entanglement in the nucleation of polymer melts, which is the unique feature of polymer differentiated from small molecules. By performing molecular dynamics…
The many-body state of carriers confined in a quantum dot is controlled by the balance between their kinetic energy and their Coulomb correlation. In coupled quantum dots, both can be tuned by varying the inter-dot tunneling and…
A new phenomenon, called cooperative internal conversion process, in which the coupling of bound-free electron and neutron transitions due to the dipole term of their Coulomb interaction permits cooperation of two nuclei leading to neutron…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they…
The Q-cycle mechanism plays an important role in the conversion of the redox energy into the energy of the proton electrochemical gradient across the biomembrane. The bifurcated electron transfer reaction, which is built into this…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
We propose to use a quantum ratchet to transport quantum information in a chain of atoms trapped in an optical superlattice. The quantum ratchet is created by a continuous modulation of the optical superlattice which is periodic in time and…
The process of protons transport in molecular water chains is of fundamental interest for many biological systems. Although many features of such systems can be analyzed using large-scale computational modeling, other features are better…
Trapped Bosons exhibit fundamental physical phenomena and are potentially useful for quantum technologies. We present a method for simulating Bosons using path integral molecular dynamics. A main challenge for simulations is including all…
The quantum-mechanical mechanisms by which the enzymes catalyze the hydrogen transfer in biochemical reactions are considered. Up to date it was established both experimentally and theoretically that in many cases the proton tunnelling…
Dynamics of molecular motors that move along linear lattices and interact with them via reversible destruction of specific lattice bonds is investigated theoretically by analyzing exactly solvable discrete-state ``burnt-bridge'' models.…
We introduce a bond percolation procedure on a $D$-dimensional lattice where two neighbouring sites are connected by $N$ channels, each operated by valves at both ends. Out of a total of $N$, randomly chosen $n$ valves are open at every…
We study a model describing some aspects of the dynamics of biopolymers. The models involve either one or two finite chains with a number N of sites that represent the "units" of a biophysical system. The mechanical degrees of freedom of…
RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on…
A system consisting of two single-mode cavities spatially separated and connected by an optical fiber and multiple two-level atoms trapped in the cavities is considered. If the atoms resonantly and collectively interact with the local…
In this paper, knot physics on entangled vortex-membranes are studied including classification, knot dynamics and effective theory. The physics objects in this paper are entangled vortex-membranes that are called composite knot-crystals.…