This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Carbon nanotubes (CNTs) are rolled sheets of graphite discoved in 1991 [99]. With narrow nano-size diameter, CNT can grow as long as several microns in length. CNTs made from a single graphite sheet are referred to as single-walled carbon nanotubes (SWNTs). Due to their superb electronic, thermal, chemical, as well as mechanical properties, SWNTs have shown extraordinary potential in bioengineering, biomedicine and nanotechnological applications, in particular, as drug delivery devices [100 102] and biosensors [103,104]. It has been shown that SWNTs can shuttle various cargo including water [105], protons [106], polymers [107], and nucleic acids [108] across cellular membranes, opening a new path for drug delivery. In addition, the optical signals of SWNTs are sensitive to environment changes. Monitoring the changes in the optical signal allows sensitive detection of target biomolecules, qualifing nanotubes as bio-sensors [103]. Theoretical and computational modeling of the interaction between SWNTs (www.ks.uiuc.edu/Research/nanotube/) and biomolecules can shed light on the properties of CNT-based nano-biological systems, and establish new concepts for controlling/tuning the performance of such systems to design and optimize these devices. To characterize the interactions between SWNTs and biomolecules in MD simulations, it is crucial to consider the polarizable nature of SWNTs due to their highly delocalized pi-electrons. To address this issue, the Resource has developed a semi-empirical method [109], namely a tight binding model, that takes into account the polarization effect of SWNTs at low computational cost. In this method, the induced atomic partial charges, i.e, the dielectric response of SWNTs, are predetermined through density functional theory calculations to improve the quality of electrostatics in the existing MD forcefield. Key properties such as electronic energy spectrum and screening constants, computed with the new tight binding approach agree well with results from first principle calculations despite its compuational simplicity [110, 111]. The method has been employed to study the systems of water-SWNTs [109 111] and ion-SWNTs [112], both of which are of fundamental importance for biological applications. In the water-SWNT systems, the atomic partial charges on the nanotube edges are found to greatly contribute to the total interaction energy, while the polarization of the SWNT significantly lowers the electrostatic energy in the center of the tube, e.g., for ions [111]. A simulation of a SWNT with a potassium ion revealed a THz oscilation of the ion, demonstrating the accuracy and efficiency of the polarizable SWNT model [98]. The Resource is currently making efforts to implement the semi-empirical method into NAMD [113], so that the electronic response of SWNTs can be evaluated on-the-fly during MD simulations. The application of this method to larger systems such as DNA-SWNT complexes are now being investigated.
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