Simulations of composite carbon films with nanotube inclusions

We study the interfacial structure, stability, and elastic properties of composite carbon films containing nanotubes. Our Monte Carlo simulations show that Van der Waals forces play a vital role in shaping up the interfacial geometry, producing a curved graphitic wall surrounding the tubes. The most stable structures are predicted to have intermediate densities, high anisotropies, and increased elastic moduli compared to pure amorphous carbon films.Comment: 3 pages, 3 figures, to appear in Appl. Phys. Let

Insights into the fracture mechanisms and strength of amorphous and nanocomposite carbon

Tight-binding molecular dynamics simulations shed light into the fracture mechanisms and the ideal strength of tetrahedral amorphous carbon and of nanocomposite carbon containing diamond crystallites, two of the hardest materials. It is found that fracture in the nanocomposites, under tensile or shear load, occurs inter-grain and so their ideal strength is similar to the pure amorphous phase. The onset of fracture takes place at weakly bonded sp^3 sites in the amorphous matrix. On the other hand, the nanodiamond inclusions significantly enhance the elastic moduli, which approach those of diamond.Comment: 6 pages, 4 figure

Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations

We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that the coupling of the correlated molecular motion to hydrodynamics results in significant acceleration of the translocation process. Based on these results, we construct a phenomenological model which incorporates the statistical and dynamical features of the translocation process and predicts a power law dependence of the translocation time on the polymer length with an exponent $\alpha$ $\approx 1.2$. The actual value of the exponent from the simulations is $\alpha = 1.28 \pm 0.01$, which is in excellent agreement with experimental measurements of DNA translocation through a nanopore, and is not sensitive to the choice of parameters in the simulation. The mechanism behind the emergence of such a robust exponent is related to the interplay between the longitudinal and transversal dynamics of both translocated and untranslocated segments. The connection to the macroscopic picture involves separating the contributions from the blob shrinking and shifting processes, which are both essential to the translocation dynamics.Comment: 7 pages, 5 figures. to appear in Phys. Rev.

Energetics and stability of nanostructured amorphous carbon

Monte Carlo simulations, supplemented by ab initio calculations, shed light into the energetics and thermodynamic stability of nanostructured amorphous carbon. The interaction of the embedded nanocrystals with the host amorphous matrix is shown to determine in a large degree the stability and the relative energy differences among carbon phases. Diamonds are stable structures in matrices with sp^3 fraction over 60%. Schwarzites are stable in low-coordinated networks. Other sp^2-bonded structures are metastable.Comment: 11 pages, 7 figure

DNA nucleotide-specific modulation of \mu A transverse edge currents through a metallic graphene nanoribbon with a nanopore

We propose two-terminal devices for DNA sequencing which consist of a metallic graphene nanoribbon with zigzag edges (ZGNR) and a nanopore in its interior through which the DNA molecule is translocated. Using the nonequilibrium Green functions combined with density functional theory, we demonstrate that each of the four DNA nucleotides inserted into the nanopore, whose edge carbon atoms are passivated by either hydrogen or nitrogen, will lead to a unique change in the device conductance. Unlike other recent biosensors based on transverse electronic transport through DNA nucleotides, which utilize small (of the order of pA) tunneling current across a nanogap or a nanopore yielding a poor signal-to-noise ratio, our device concept relies on the fact that in ZGNRs local current density is peaked around the edges so that drilling a nanopore away from the edges will not diminish the conductance. Inserting a DNA nucleotide into the nanopore affects the charge density in the surrounding area, thereby modulating edge conduction currents whose magnitude is of the order of \mu A at bias voltage ~ 0.1 V. The proposed biosensor is not limited to ZGNRs and it could be realized with other nanowires supporting transverse edge currents, such as chiral GNRs or wires made of two-dimensional topological insulators.Comment: 6 pages, 6 figures, PDFLaTe

Transverse Electronic Transport through DNA Nucleotides with Functionalized Graphene Electrodes

Graphene nanogaps and nanopores show potential for the purpose of electrical DNA sequencing, in particular because single-base resolution appears to be readily achievable. Here, we evaluated from first principles the advantages of a nanogap setup with functionalized graphene edges. To this end, we employed density functional theory and the non-equilibrium Green's function method to investigate the transverse conductance properties of the four nucleotides occurring in DNA when located between the opposing functionalized graphene electrodes. In particular, we determined the electrical tunneling current variation as a function of the applied bias and the associated differential conductance at a voltage which appears suitable to distinguish between the four nucleotides. Intriguingly, we observe for one of the nucleotides a negative differential resistance effect.Comment: 19 pages, 7 figure

Lattice Boltzmann simulations of soft matter systems

This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief explanation of the concept of hydrodynamic interactions, we give a general overview over the various simulation methods that have been developed to cope with the resulting computational problems. We then focus on the approach we have developed, which couples a system of particles to a lattice Boltzmann model representing the solvent degrees of freedom. The standard D3Q19 lattice Boltzmann model is derived and explained in depth, followed by a detailed discussion of complementary methods for the coupling of solvent and solute. Colloidal dispersions are best described in terms of extended particles with appropriate boundary conditions at the surfaces, while particles with internal degrees of freedom are easier to simulate as an arrangement of mass points with frictional coupling to the solvent. In both cases, particular care has been taken to simulate thermal fluctuations in a consistent way. The usefulness of this methodology is illustrated by studies from our own research, where the dynamics of colloidal and polymeric systems has been investigated in both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures, 76 page

Assessment of Seroconversion after SARS-CoV-2 Vaccination in Patients with Lung Cancer

Background: SARS-CoV-2 mortality rates are significantly higher in patients with lung cancer compared with the general population. However, little is known on their immunization status after vaccination. Methods: To evaluate the humoral response (seroconversion) of patients with lung cancer following vaccination against SARS-COV-2 (Group A), we obtained antibodies against SARS-CoV-2 spike (S) protein both at baseline and at different time points after the first dose of SARS-CoV-2 vaccine (two to three weeks [T1], six weeks ± one week [T2], 12 weeks ± three weeks [T3], and 24 weeks ± three weeks [T4]). Antibodies were also acquired from a control cohort of non-lung cancer patients (Group B) as well as a third cohort containing healthy controls (Group C) at all time points and at T4, respectively, to make comparisons with Group A. Analysis of antibody response at different time points, association with clinicopathologic parameters, and comparisons with control groups were performed. Results: A total of 125 patients with lung cancer were included in the analysis (96 males [74.3%], median age of 68 years [46–91]. All study participants received two vaccine doses (BNT162b2, mRNA-1273, AZD1222). Analysis of anti-SARS-CoV-2 S antibody titers showed minimal response at T1 (0.4 [0.4–48.6] IU/mL). Antibody response peaked at T2 (527.0 [0.4–2500] IU/mL) and declined over T3 (323.0 [0.4–2500] IU/mL) and T4 (141.0 [0.4–2500] IU/mL). Active smokers had lower antibody titers at T2 (p = 0.04), T3 (p = 0.04), and T4 (p < 0.0001) compared with former or never smokers. Peak antibody titers were not associated with any other clinicopathologic charac-teristic. No significant differences were observed compared with Group B. However, lung cancer patients exhibited significantly decreased antibody titers compared with Group C at T4 (p < 0.0001). Conclusions: Lung cancer patients demonstrate sufficient antibody response six weeks after the first dose of vaccine against SARS-CoV-2 when vaccinated with two-dose regimens. Rapidly declining antibody titers six weeks after the first dose underline the need for a third dose three months later, in patients with lung cancer, and especially active smokers. © 2022 by the authors. Licensee MDPI, Basel, Switzerland