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In this work we report the study of conformation dependent electronic transport properties of DNA double-helix within tight-binding framework including its helical symmetry. We have studied the changes in localization properties of DNA as…
Understanding the motion of particles with ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or…
We investigate dynamical heterogeneities in the collective relaxation of a concentrated microgel system, for which the packing fraction can be conveniently varied by changing the temperature. The packing fraction dependent mechanical…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…
Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to…
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase…
We describe a hybrid molecular dynamics approach for the description of ultracold neutral plasmas, based on an adiabatic treatment of the electron gas and a full molecular dynamics simulation of the ions, which allows us to follow the…
Due to the redundant nature of DNA synthesis and sequencing technologies, a basic model for a DNA storage system is a multi-draw "shuffling-sampling" channel. In this model, a random number of noisy copies of each sequence is observed at…
We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The…
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…
The evolution of particulate and multiphase systems can transition from dynamic regimes, governed by classical transport equations with well-defined damping coefficients, to anomalously slow relaxation described by rate equations when the…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i)…
Ionic behaviors, including ion distributions and hydration characteristics at solid-liquid interfaces, are important research interests in many important applications, such as electric double-layer capacitors and water lubrication. Here, we…
We used high-resolution quasielastic neutron scattering spectroscopy to study the single-particle dynamics of water molecules on the surface of hydrated DNA samples. Both H2O and D2O hydrated samples were measured. The contribution of…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
Electron microscopy and X-ray diffraction studies of dormant E. coli cells revealed several forms of nucleoid condensation: quasi - nanocrystalline, quasi -liquid crystalline (or spore-like) and folded nucleosome - like structure. Of…
The volume occupied by the unconstrained genomic DNA of prokaryotes in saline solutions is thousand times larger than the cell. Moreover, it is not separated from the rest of the cell by a membrane. Nevertheless, it occupies only a small…
Encapsulation of dsDNA fragments (contour length 54 nm) by the cationic diblock copolymer poly(butadiene-b-N-methyl 4-vinyl pyridinium) [PBd-b-P4VPQ] has been studied with phase contrast, polarized light, and fluorescence microscopy, as…
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…