{"id":217,"date":"2023-08-02T19:48:44","date_gmt":"2023-08-03T02:48:44","guid":{"rendered":"https:\/\/dornsife.usc.edu\/compbionano\/?page_id=217"},"modified":"2023-08-02T19:48:53","modified_gmt":"2023-08-03T02:48:53","slug":"research-interests","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/compbionano\/research-interests\/","title":{"rendered":"Research focus"},"content":{"rendered":"\n\n \n \n\n\n\n\n\n\n\n
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Theoretical and computational physics of matter, with emphasis on ab-initio studies of biological molecules and molecules interacting with surfaces. Specific topics include:<\/p>\n

1\u00a0\u00a0\u00a0\u00a0\u00a0 Capabilities, limits and extensions of solid-state computational tools (DFT and tight-binding) to study biomolecules appealing for electronic applications. The investigated biomolecules are: (i) natural and modified nucleic acids; (ii) copper metalloproteins; (iii) model b-sheet peptides on solid surfaces in a wet environment.<\/p>\n

2\u00a0\u00a0\u00a0\u00a0\u00a0 Theory of charge mobility in biomolecules: links between the solid-state-like charge transport through extended orbitals and the charge transfer between localized molecular sites (Marcus-Hush-Jortner Theory).<\/p>\n

3\u00a0\u00a0\u00a0\u00a0\u00a0 Methodological development to compute electron transfer rates in biomolecular systems within density functional theory. Application to: (i) electron exchange between two electron transfer proteins in an azurin dimer; (ii) hole exchange between two adjacent planes in stacked dimers of duplex and quadruplex DNA, as well as chemically modified DNA, with different sequences.<\/p>\n

4\u00a0\u00a0\u00a0\u00a0\u00a0 Use of molecular dynamics simulations to sample the conformational effects on the electronic and optical properties of biological molecules. Application to DNA duplexes, triplexes, tetraplexes and duplexes with non-natural bases.<\/p>\n

5\u00a0\u00a0\u00a0\u00a0\u00a0 Role of the solvent in the electronic structure and charge properties of DNAs and proteins. Investigation of a continuum solvent and discrete coordination water molecules.<\/p>\n

6\u00a0\u00a0\u00a0\u00a0\u00a0 Optical absorption and circular dichroism of chiral molecules including natural and modified DNAs.<\/p>\n

7\u00a0\u00a0\u00a0\u00a0\u00a0 DFT-based parametrization of classical force fields for modified nucleobases and for protein-surface and DNA-surface interaction.<\/p>\n

8\u00a0\u00a0\u00a0\u00a0\u00a0 DFT studies of the adsorption of organic molecules and biomolecules on metal surfaces, with aromatic and alkylic molecules, in the diluted coverage range and in the range of self-assembled-monolayers: nucleobases\/Au(111), amino-acids\/Au(111), methanethiol\/Au(111), pentacene\/Cu(100), DPDI\/Cu(111), mercaptobenzoxazole\/Cu(100), and others. Different regimes of molecule-metal hybridization from chemisorption to weak interaction.<\/p>\n

9\u00a0\u00a0\u00a0\u00a0\u00a0 Molecular dynamics simulations of protein-binding DNA oligomers and of protein-DNA bound complexes.<\/p>\n

10\u00a0\u00a0 Electronic structure of organic and inorganic polymers that can serve as new nanowires for electronic applications. Free-standing polymers, interfaces with metal surfaces, and junctions with two metal electrodes. Current investigations are devoted to specific polymers MMX (metal-metal-halogen chains that coordinate various lateral organic groups) and MoSI compounds.<\/p>\n

11\u00a0\u00a0 Methodological development to address excited-state transport mechanisms, as well as dispersion interactions for a suitable description of molecule-molecule and molecule-inorganic coupling.<\/p>\n

12\u00a0\u00a0 Ab-initio theory and empirical modeling of the structure, electronic properties and optical excitations of hybrid metal\/semiconductor interfaces and nanoparticles (nano-dumbbells).<\/p>\n

13\u00a0\u00a0 Impact of quantum computation on nanosciences spanning chemistry, materials science, physics and biology.<\/p>\n

Many of these activities include direct collaboration with experimental groups for guidance and interpretation.<\/p>\n

For details oof ongoing projects, see the\u00a0Research<\/a> page.<\/p>\n<\/div>\n\n\n\n<\/div>\n\n\n <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":354,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-content-detail.php","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-217","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"\nResearch focus - CompBioNano<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/dornsife.usc.edu\/compbionano\/research-interests\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Research focus - CompBioNano\" \/>\n<meta property=\"og:url\" content=\"https:\/\/dornsife.usc.edu\/compbionano\/research-interests\/\" \/>\n<meta property=\"og:site_name\" content=\"CompBioNano\" \/>\n<meta property=\"article:modified_time\" content=\"2023-08-03T02:48:53+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/dornsife.usc.edu\/compbionano\/research-interests\/\",\"url\":\"https:\/\/dornsife.usc.edu\/compbionano\/research-interests\/\",\"name\":\"Research focus - 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