Related papers: Reactive Molecular Dynamics Simulation on DNA Doub…
We perform a comprehensive phenomenological analysis of the Scale Invariant Two Higgs Doublet Model (\textit{SI2HDM})~\cite{Lee:2012jn}. In this framework, the electroweak symmetry breaking is triggered radiatively, and the entire scalar…
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…
Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…
We discuss the role of water bridging the DNA-enzyme interaction by resorting to recent results showing that London dispersion forces between delocalized electrons of base pairs of DNA are responsible for the formation of dipole modes that…
The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA…
We propose a scheme that generates period-doubled responses via periodically driving certain Hamiltonians hosting quantum many-body scars, akin to recent experimental observations in driven Rydberg atom arrays. Our construction takes…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
The rapid worldwide spread of severe viral infections, often involving novel modifications of viruses, poses major challenges to our health care systems. This means that tools that can efficiently and specifically diagnose viruses are much…
We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…
The nuclear shell model is one of the successful models in theoretical understanding of nuclear structure. If a convenient effective interaction can be found between nucleons, various observables such as energies of nuclear states are…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded block copolymer DNA with $-A_n B_n-$ repeat units. Here $A$ and $B$ represent two different types of base pairs having two- and three-bonds,…
We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
1D and 2D supernova simulations for stars between 11 and 25 solar masses are presented, making use of the Prometheus/Vertex neutrino-hydrodynamics code, which employs a full spectral treatment of the neutrino transport. Multi-dimensional…
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…
In Paper I, we followed the evolution of binary stars as they orbited near the supermassive black hole (SMBH) at the Galactic center, noting the cases in which the two stars would come close enough together to collide. In this paper we…
To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel…
The genomic DNA of most bacteria is significantly underwound, which constrains the DNA molecule to adopt a branched plectoneme geometry. Moreover, biological functions like replication and transcription require that the two DNA strands be…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Charge transfer can take place along double helical DNA over distances as long as 30 nanometers. However, given the active role of the thermal environment surrounding charge carriers in DNA, physical mechanisms driving the transfer process…