Supriyo Naskar

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.

Peptide nucleic acids (PNAs) are charge-neutral polyamide oligomers having extremely favorable thermal stability and high affinity to cell membranes when coupled with cationic cell-penetrating peptides (CPPs), as well as the encouraging antisense and antigene activity in cell-free systems. The study of the mechanical properties of short PNA molecules is rare both in experiments and theoretical calculations. Here, we studied the microscopic structures and elastic properties; namely, persistence length, stretch modulus, twist–stretch coupling, and structural crookedness of double-stranded PNA (dsPNA) and their hybrid derivatives using all-atom MD simulation and compared them with those of double-stranded DNA (dsDNA) and double-stranded RNA (dsRNA). The stretch modulus of the dsPNA is found to be ∼160 pN, an order of magnitude lower than that of dsDNA and smaller than dsRNA, respectively. Similarly, the persistence length of dsPNA is found to be ∼35 nm, significantly smaller than those of dsDNA and dsRNA. The PNA–DNA and PNA–RNA hybrid duplexes have elastic properties lying between that of dsPNA and dsDNA/dsRNA. We argue that the neutral backbones of the PNA make it less stiff than dsDNA and dsRNA molecules. Measurement of structural crookedness and principal component analysis additionally support the bending flexibility of dsPNA. Detailed analysis of the helical-rise coupled to helical-twist indicates that the PNA–DNA hybrid over-winds like dsDNA, while PNA–PNA and PNA–RNA unwind like dsRNA upon stretching. Because of the highly flexible nature of PNA, it can bind other biomolecules by adopting a wide range of conformations and is believed to be crucial for future nanobiotechnology research studies.

An artificial template mediated fabrication of secondary structure within peptides always attracts great interest in biological system due to its several biomimetic interactions. In all earlier studies, an uniform template containing molecules/nanomaterials were used to target only one type of peptide at a time which extensively limits the diversity in the generation of artificial protein surface/receptors. This limitation can be overcome by the incorporation of more than one binding template (heterogenity) in a single system, for example Janus nanomaterials, which is challenging and difficult to synthesize. In this context, graphene oxide (GO) was considered as an artificial receptor (template). It contains two distinctive binding zones i.e., surface and edge, which can induce the secondary structure of peptides based on complimentary interactions. To establish our concept, we have implemented a hybrid sequence i.e., i, i+4, i+7 and i+11 pattern peptides which defines a more linear surface, suitable for recognition by the two-dimensional GO. Depending on the amino acid residue at the specific locations, we observed substantial enhancement of peptide helicity either at the surface or edges of GO from the random coil. However, non-interacting peptide remains as random coil. We have established this by circular dichroism study at various conditions, as well as atomic force microscopy and optical imaging study. Furthermore, we have also established our observation using molecular dynamics (MD) simulations. This study reveals that synthesized GO-peptides composite with different secondary structures and recognition residues can mimic biological systems.

The unique sequence specificity rule of DNA makes it an ideal molecular building block for constructing periodic arrays and devices with nanoscale accuracy and precision. Here, we present the self-assembly of DNA nanostars having three, four and five arms into a gel phase using a simplistic coarse-grained bead-spring model developed by Z. Xing, C. Ness, D. Frenkel and E. Eiser (Macromolecules, 2019, 52, 504–512). Our simulations show that the DNA nanostars form a thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as the radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from an arrested gel phase to an unstructured liquid phase has been modelled using a two-state theoretical model. We find that this transition is enthalpy driven, and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends, which gives rise to a gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using a two-phase thermodynamic model, also substantiates the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature demonstrates the phase transition to a gel phase. A detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, is easily extensible to other polymeric systems, and is expected to help in understanding the physics of self-assembly.

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.

A series of linker-substituted ultramicroporous CALF-20 metal–organic frameworks (MOFs) were built in silico, and their CO_2 capture performances over N2 in flue gas conditions were systematically computationally explored. Among the various linker substitutions explored, squarate-linker-incorporated CALF-20 (SquCALF-20) was demonstrated to show a larger CO2 uptake at 0.15 bar (3.6 mmol/g) and higher CO2/N2 selectivity (500) in dry conditions compared to pristine CALF-20. Interestingly, this MOF was shown to maintain a high level of CO2 capture performance even in the presence of humidity, although it starts to adsorb H2O at lower relative humidity compared to CALF-20. Because squaric acid is a semiconductor industry feedstock and the few-already published squarate-based MOFs are chemically robust, this engineered SquCALF-20 offers a promising avenue for cost-effective CO2 capture via physisorption, with potential applications in addressing environmental concerns associated with CO2 emissions.

The separation of high-value-added chemicals from organic solvents is of prime importance for many industries but it is associated with a large energy consumption penalty. Suitably, membrane-based nanofiltration offers potential for a more energy-efficient separation than the conventional energy-intensive thermal processes. Conceivably, mixed-matrix membranes (MMMs), encompassing metal-organic frameworks (MOFs) as fillers, are poised to promote selective separation via molecular sieving, synergistically combining polymers flexibility and fine-tuned porosity of MOFs. Nevertheless, conventional direct mixing of MOFs with polymer solutions results in underutilization of the MOF fillers owing to their uniform cross-sectional distribution. Therefore, in this work, we propose a multizoning technique for the formation of MMMs with an asymmetric-filler density at the macroscale, in which the MOF fillers are distributed only on the surface of the membrane, and a seamless interface at the nanoscale. Our design strategy demonstrates five times higher MOF surface coverage, which results in a solvent permeance five times higher than that of conventional MMMs while maintaining high selectivity. Practically, MOFs are paired with polymers of similar chemical nature in order to enhance their adhesion without the need for additional surface modification. Our approach offers permanently accessible MOF porosity, which translates to effective molecular sieving, as exemplified by the polybenzimidazole and Zr-BI-fcu-MOF system. Our findings pave the way for the development of composite materials with a seamless interface.