Supriyo Naskar

The DNA molecule, apart from carrying the genetic information, plays a crucial role in a variety of biological processes and finds applications in drug design, nanotechnology and nanoelectronics. The molecule undergoes significant structural transitions under the influence of forces due to physiological and non-physiological environments. Here, we summarize the insights gained from simulations and single-molecule experiments on the structural transitions and mechanics of DNA under force, as well as its elastic properties, in various environmental conditions, and discuss appealing future directions.

The flexibility and stiffness of small DNA molecules play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) with lengths ranging from 12 base-pairs (bp) to 56 bp, paranemic crossover (PX) DNA and hexagonal DNA nanotubes (DNTs) using two widely used coarse-grained models – Martini and oxDNA. To calculate the persistence length (Lp) and the stretch modulus (γ) of the dsDNA, we incorporate the worm-like chain and elastic rod model, while for the DNTs, we implement our previously developed theoretical framework. We compare and contrast all of the results with previously reported all-atom molecular dynamics (MD) simulations and experimental results. The mechanical properties of dsDNA (Lp ∼ 50 nm, γ ∼ 800–1500 pN), PX DNA (γ ∼ 1600–2000 pN) and DNTs (Lp ∼ 1–10 μm, γ ∼ 6000–8000 pN) estimated using the Martini soft elastic network and oxDNA are in very good agreement with the all-atom MD and experimental values, while the stiff elastic network Martini reproduces values of Lp and γ which are an order of magnitude higher. The high flexibility of small dsDNA is also depicted in our calculations. However, Martini models proved inadequate to capture the salt concentration effects on the mechanical properties with increasing salt molarity. oxDNA captures the salt concentration effect on the small dsDNA mechanics. But it is found to be ineffective for reproducing the salt-dependent mechanical properties of DNTs. Also, unlike Martini, the time evolved PX DNA and DNT structures from the oxDNA models are comparable to the all-atom MD simulated structures. Our findings provide a route to study the mechanical properties of DNA and DNA based nanostructures with increased time and length scales and has a remarkable implication in the context of DNA nanotechnology.

The traditional synthesis method produces microcrystalline powdered MOFs, which prevents direct implementation in real-world applications which demand strict control of shape, morphology and physical properties. Therefore, shaping of MOFs via the use of binders is of paramount interest for their practical use in gas adsorption/separation, catalysis, sensors, etc. However, so far, the binders have been mostly selected by trial-and-error without anticipating the adhesion between the MOF and binder components to ensure the processability of homogeneous and mechanically stable shaped MOFs and the impact of the shaping on the intrinsic properties of the MOFs has been overlooked. Herein, we deliver a first systematic multiscale computational exploration of MOF/binder composites by selecting CALF-20, a prototypical MOF for real application in the field of CO2 capture, and a series of binders that cover a rather broad spectrum of properties in terms of rigidity/flexibility, porosity, and chemical functionality. The adhesion between the two components and hence the effectiveness of the shaping as well as the impact of the overall porosity of the CALF-20/binder on the CO2/N2 selectivity, CO2 sorption capacity and kinetics was analyzed. Shaping of CALF-20 by carboxymethyl cellulose was predicted to enable a fair compromise between excellent adhesion between the two components, whilst maintaining high CO2/N2 selectivity, large CO2 uptake and CO2 transport as fast as in the CALF-20. This multiscale computational tool paves the way towards the selection of an appropriate binder to achieve an optimum shaping of a given MOF in terms of processability whilst maintaining its high level of performance.

CALF-20 was recently identified as a novel benchmark sorbent for CO2 capture at the industrial scale, however comprehensive atomistic insight into its mechanical/thermal properties under working conditions is still lacking. In this study, we developed a general-purpose machine-learned potential (MLP) for the CALF-20 MOF framework that predicts the thermodynamic and mechanical properties of the structure at finite temperatures within first-principles accuracy. Interestingly, CALF-20 was demonstrated to exhibit both negative area compression and negative thermal expansion. Most strikingly, upon application of the tensile strain along the [001] direction, CALF-20 was shown to display a distinct two-step elastic deformation behavior, unlike typical MOFs that undergo plastic deformation after elasticity. Furthermore, this MOF was shown to exhibit a spectacular fracture strain of up to 27% along the [001] direction at room temperature comparable to that of MOF glasses. These abnormal thermal and mechanical properties make CALF-20 as attractive material for flexible and stretchable electronics and sensors.