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Super-resolution imaging based on single molecule localization allows accessing nanometric-scale information in biological samples with high precision. However, complete measurements including molecule orientation are still challenging.…
A molecular rotation assisted non-sequential double ionization (MR-NSDI) mechanism is identified in the breakup of rotational H$_2$ molecules in a few-cycle intense laser pulse using a semi-classical trajectory Monte Carlo method. Applying…
Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
We combine experiments and theory to investigate the orientational dynamics of dipolar ellipsoids, which self-assemble into elongated ribbon-like structures due to the presence in each particle of a permanent magnetic moment perpendicular…
Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
We report on theoretical studies of electronic transport in the archetypical molecular hybrid formed by DNA wrapped around single-walled carbon nanotubes (CNTs). Using a Green's function formalism in a $\pi$-orbital tight-binding…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
Biological molecules are characterized by an intrinsic asymmetry known as homochirality. The result is optical activity of biological materials and circular polarization in the light scattered by microorganisms, cells of living organisms,…
Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In…
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…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
DNA-coated colloids are a popular model system for self-assembly through tunable interactions. The DNA-encoded linkages between particles theoretically allow for very high specificity, but generally no directionality or long-range…
The frontier orbital sequence of individual dicyanovinyl-substituted oligothiophene molecules is studied by means of scanning tunneling microscopy. On NaCl/Cu(111) the molecules are neutral and the two lowest unoccupied molecular states are…
The mixed-field orientation of an asymmetric-rotor molecule with its permanent dipole moment non-parallel to the principal axes of polarizability is investigated experimentally and theoretically. We find that for the typical case of a…
The microscopic orientation and position of photoactive molecules is crucial to the operation of optoelectronic devices such as OLEDs and solar cells. Here, we introduce a shape-persistent macrocyclic molecule as an excellent fluorescent…