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Layered two-dimensional (2D) materials exhibit unique properties, expanding opportunities in material design. We investigate MX$_2$ transition metal dichalcogenides (TMDCs) (M = Mo, W; X = S, Se, Te) in homo- and heterobilayers with…
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
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…
We investigate the charge transfer characteristics of one and two excess charges in a DNA base-pair dimer using a model Hamiltonian approach. The electron part comprises diagonal and off-diagonal Coulomb matrix elements such a correlated…
For coupled-dimer magnets with quenched disorder, we introduce a generalization of the bond-operator method, appropriate to describe both singlet and magnetically ordered phases. This allows for a numerical calculation of the magnetic…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Hexagonal boron nitride ($\it h$-BN) exhibits dominant $\pi$-bands near the Fermi level, similar to graphene. However, unlike graphene, where tight-binding (TB) models accurately reproduce band edges near the $K$ and $K^{\prime}$ points in…
Single-molecule force-extension experiments have allowed quantitative measurements of the mechanical responses of biomolecules to applied forces explaining their roles in key biological functions. Electrophoretic stretching of charged…
We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of non-empirically tuned range-separated functionals, for predicting a diverse set of electronic…
We study the interplay of intrinsic-electronic and environmental factors on long-range charge transport across molecular chains with up to $N\sim 80$ monomers. We describe the molecular electronic structure of the chain with a tight-binding…
In the Hermitian regime, the Wannier-Stark ladder characterizes the eigenstates of an electron in a periodic potential with an applied static electric field. In this work, we extend this concept to the complex regime for a periodic…
Lattice reconstruction in twisted transition-metal dichalcogenide (TMD) bilayers gives rise to piezo- and ferroelectric moir\'e potentials for electrons and holes, as well as a modulation of the hybridisation across the bilayer. Here, we…
We study the metastability, internal frequencies, activation mechanism, energy transfer, and the collective base-flipping in a mesoscopic DNA via resonance with specific electric fields. Our new mesoscopic DNA model takes into account not…
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 develop a theoretical framework on the mechanism of combinatorial binding of transcription factors (TFs) with their specific binding sites on DNA. We consider three possible mechanisms viz. monomer, hetero-oligomer and coordinated…
Mixtures of polymers of varying topologies and stiffnesses display complex emergent rheological properties that often cannot be predicted from their single-component counterparts. For example, entangled blends of ring and linear polymers…
Transition metal dichalcogenide (TMD) bilayers are a new class of tunable moir\'e systems attracting interest as quantum simulators of strongly-interacting electrons in two dimensions. In particular, recent theory predicts that the…