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  • 1.
    Hu, Wei
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Duan, Sai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical modeling of surface and tip-enhanced Raman spectroscopies2017In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 7, no 2, article id UNSP e1293Article, review/survey (Refereed)
    Abstract [en]

    Raman spectroscopy is a powerful technique in molecular science because of the ability of providing vibrational 'finger-print'. The developments of the surfaceenhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) have significantly improved the detection sensitivity and efficiency. However, they also introduce complications for the spectral assignments, for which advanced theoretical modeling has played an important role. Here we summarize some of our recent progresses for SERS and TERS, which generally combine both solid-state physics and quantum chemistry methods with two different schemes, namely the cluster model and the periodic boundary condition (PBC) model. In the cluster model, direct Raman spectra calculations are performed for the cluster taken from the accurate PBC structure. For PBC model, we have developed a quasianalytical approach that enables us to calculate the Raman spectra of entire system. Under the TERS condition, the non-uniformity of plasmonic field in real space can drastically alter the interaction between the molecule and the light. By taking into account the local distributions of the plasmonic field, a new interaction Hamiltonian is constructed and applied to model the super-high-resolution Raman images of a single molecule. It shows that the resonant Raman images reflect the transition density between ground and excited states, which are generally vibrational insensitive. The nonresonant Raman images, on the other hand, allow to visualize the atomic movement of individual vibrational modes in real space. The inclusion of non-uniformity of plasmonic field provides ample opportunities to discover new physics and new applications in the future. 

  • 2. Liang, L.
    et al.
    Hu, Wei
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xue, Z.
    Shen, J. -W
    Theoretical study on the interaction of nucleotides on two-dimensional atomically thin graphene and molybdenum disulfide2017In: FlatChem, ISSN 2452-2627, Vol. 2, p. 8-14Article in journal (Refereed)
    Abstract [en]

    In this work, the interaction between single nucleotide and polynucleotides composed of different nucleotides and two-dimensional (2D) materials (graphene and MoS2) were investigated through first principles calculations and molecular dynamics (MD) simulation. The binding energy strength between single nucleotide and graphene is G > C > A > T, and it is G > A > C > T between single nucleotide and MoS2, derived from density function density (DFT) calculations. The binding strength between polynucleotide and graphene is A6 > G6 > T6 > C6, and the order is G6 > A6 > C6 > T6 of binding strength between polynucleotide and MoS2, calculated from molecular dynamics simulation. The average binding free energy for different single nucleotide A, T, C, G (polynucleotides A6, T6, C6, G6) on graphene sheet is −4.17 kcal/mol (-10.04 kcal/mol), and it is about −2.29 kcal/mol (-2.24 kcal/mol) on MoS2 surface. The binding strength for different single nucleotide (polynucleotides) on graphene sheets is around 2 times (4 times) stronger than that between nucleotide (polynucleotides) and MoS2 surface. The different absorption strength of nucleotides on these two-dimensional materials may be utilized for different promising applications.

  • 3. Liang, Lijun
    et al.
    Hu, Wei
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Zhisen
    Shen, Jia-Wei
    Theoretic Study on Dispersion Mechanism of Boron Nitride Nanotubes by Polynucleotides2016In: SCIENTIFIC REPORTS, ISSN 2045-2322, Vol. 6, article id 39747Article in journal (Refereed)
    Abstract [en]

    Due to the unique electrical and mechanical properties of boron nitride nanotubes (BNNT), BNNT has been a promising material for many potential applications, especially in biomedical field. Understanding the dispersion of BNNT in aqueous solution by biomolecules is essential for its use in biomedical applications. In this study, BNNT wrapped by polynucleotides in aqueous solution was investigated by molecular dynamics (MD) simulations. Our results demonstrated that the BNNT wrapped by polynucleotides could greatly hinder the aggregation of BNNTs and improve the dispersion of BNNTs in aqueous solution. Dispersion of BNNTs with the assistance of polynucleotides is greatly affected by the wrapping manner of polynucleotides on BNNT, which mainly depends on two factors: the type of polynucleotides and the radius of BNNT. The interaction between polynucleotides and BNNT(9, 9) is larger than that between polynucleotides and BNNT(5, 5), which leads to the fact that dispersion of BNNT(9, 9) is better than that of BNNT(5, 5) with the assistance of polynucleotides in aqueous solution. Our study revealed the molecular-level dispersion mechanism of BNNT with the assistance of polynucleotides in aqueous solution. It shades a light on the understanding of dispersion of single wall nanotubes by biomolecules.

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