Related papers: Dynamical phase transition of a periodically drive…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
Recent studies have shown that one-dimensional driven systems can exhibit phase separation even if the dynamics is governed by local rules. The ABC model, which comprises three particle species that diffuse asymmetrically around a ring,…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…
We determine the phase diagram of DNA with inter- and intra-strand native-pair interactions that mimic the compaction of DNA. We show that DNA takes an overall sheet-like structure in the region where an incipient transition to a compact…
The denaturation of double-stranded DNA as function of force and temperature is discussed. At room temperature, sequence heterogeneity dominates the physics of single molecule force-extension curves starting about 7 piconewtons of below a…
Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the…
Time-dependently driven stochastic systems form a vast and manifold class of non-equilibrium systems used to model important applications on small length scales such as bit erasure protocols or microscopic heat engines. One property that…
A dynamic phase transition (DPT) with respect to the period P of an applied alternating magnetic field has been observed previously in numerical simulations of magnetic systems. However, experimental evidence for this DPT has thus far been…
Understanding the magnetization switching process in ferromagnetic thin films is essential for many technological applications. We investigate the effects of periodic driving via magnetic fields on a macrospin system under explicit…
The dynamics of a two-state system whose energies undergo a real crossing at some instant of time is studied. At this instant, both the coupling and the detuning vanish simultaneously, which leads to an exact degeneracy of the eigenenergies…
We investigate the efficient learning of magnetic phases using artificial neural networks trained on synthetic data, combining computational simplicity with physics-informed strategies. Focusing on the diluted Ising model, which lacks an…
Driven diffusive systems have provided simple models for non-equilibrium systems with non-trivial structures. Steady state behaviour of these systems with constant boundary conditions have been studied extensively. Comparatively less work…
We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature "slot," and always proceeds via a two-step process, mediated by…
We study the dynamical magnetization process in the ordered ground-state phase of the transverse Ising model under sweeps of magnetic field with constant velocities. In the case of very slow sweeps and for small systems studied previously…
Literature data on the properties of DNA open states are reviewed and analyzed. These states are formed as a result of strong DNA fluctuations and have a great impact on a number of biochemical processes; among them is charge transfer in…
We study different configurations of permanent magnets and ferromagnetic circuit, in order to optimize the magnetic field for the so-called ``magnetic tweezers'' technique, for studing mechanical properties of DNA molecules. The magnetic…
We numerically examine the dynamic phases and pattern formation of two-dimensional monodisperse repulsive disks driven over random quenched disorder. We show that there is a series of distinct dynamic regimes as a function of increasing…
This review focuses on the force-induced unzipping transition of double-stranded DNA. It begins with a brief history of DNA melting, which emerged alongside the growth of the field of molecular biology, juxtaposed with the advancements in…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a…