Affiliations:

• Tulane Cancer Center
• Tulane Vector Borne Infectious Diseases Research Center
• Tulane Lung Biology Program
• Tulane Bio-innovation Program

Research interests include Nanobiotechnology, Molecular Recognition and Self-Assembly.

Exquisitely controlled self-assembly in water is a key modality used by Nature to build highly functional biological systems. Research in the Jayawickramarajah group involves a highly interdisciplinary effort to develop bio-inspired functional molecules capable of undergoing specific molecular recognition events. A main thrust of our research is to study water compatible, self-assembling, synthetically functionalized oligomers that address contemporary problems.  We are currently focused on the following research areas.

1. The Chemistry and Self-Assembly of Macrocyclic Host-DNA Conjugates. The focus of our scientific research is at the interface of supramolecular chemistry with biology and materials. In particular, we have recently pioneered the nascent field of Host-DNA conjugates. This field involves the imbrication of synthetic macrocyclic hosts with DNA sequences. Such chimeric systems can exploit the programmability and controllability of DNA with the orthogonal molecular recognition and interesting functionality of synthetic hosts leading to highly functional and dynamic assemblies (e.g., input-responsive nanomachines and biomarker triggered protein inhibitors) that thrive in aqueous environments. Robust molecular recognition in water is a critical strength since most synthetic molecular recognition systems fail in water (as a result of insolubility issues and/or competing interactions with water).

Representative Publications

Kankanamalage, D. V. D. W.; Tran, J. H. T.; Beltrami, N.; Meng, K.; Zhou, X.; Pathak, P.; Isaacs, L,; Burin, A. L.; Ali, M. F.; Jayawickramarajah, J. DNA strand displacement driven by host-guest interactions. J. Am. Chem. Soc. 2022. DOI:10.1021/jacs.2c05726.

Pandey, S.; Kankanamalage, D.; Zhou, X.; Hu, C.; Isaacs, L,; Jayawickramarajah, J.; Mao, H. Chaperone assisted host-guest interactions revealed by single-molecule force spectroscopy. J. Am. Chem. Soc. 2019. 141, 18395-18389. DOI:10.1021/jacs.9b09019.

Zhou, X.; Pathak. P.; Jayawickramarajah, J. Design, synthesis, and applications of DNA-macrocyclic host conjugates. Chem Comm. 2018, 54, 11668-11680. DOI: 10.1039/c8cc06716c.

2. Bright, Non-Aggregating, Porphyrin/Fluorophore Arrays. The antenna complexes used in natural photosynthesis are predominantly composed of densely packed light-absorbing porphyrin-like pigments (chlorophyll- or bacteriochlorophyll-pigments) that are specifically positioned, and protected from self-stacking, by self-assembling peptide scaffolds. While nature has mastered the construction of exquisite photonic self-assemblies that are densely packed with chromophores, a long-standing hurdle that needs to be overcome to fully develop synthetic nanostructures composed of arranged chromophores (especially in water) is the minimization of dye-dye aggregation. Such dye contact can significantly attenuate the photophysical properties of the chromophores (e.g., quenching of excited states) thereby precluding the use of the excited state for subsequent processes. As importantly, increasing dye density can substantially compromise the nanostructured assembly due to competing hydrophobic interactions and even result in the formation of ill-defined aggregates and precipitates. Our group has constructed synthetic (and photonic) nanostructures, including nanowires and nanospheres wherein macrocycle (e.g., cyclodextrin) based host-guest interactions are used to prevent chromophore aggregation.

Representative Publications

Pathak, P.; Zarandi, M. A.; Zhou, X.; Jayawickramarajah, J. Synthesis and applications of porphyrin-biomacromolecule conjugates. Front. Chem. 2021, 9, 764137. DOI: 10.3389/fchem.2021.764137

Pathak, P.; Yao, W.; Hook, K. D.; Vik, R.; Winnerdy, F. R.; Brown, J. Q.; Gibb, B. C.; Pursell, Z F.; Phan, A. T.; Jayawickramarajah, J. Bright G-quadruplex nanostructures functionalized with porphyrin lanterns. J. Am. Chem. Soc. 2019, 141, 12582-12591. DOI: 10.1021/jacs.9b03250.

Zhang, H.; Zhang, B.; Zhu, M.; Grayson, S.; Schmehl, R.; Jayawickramarajah, J. Water-soluble porphyrin nanospheres: Enhanced photo-physical properties achieved via cyclodextrin driven double self-inclusion, Chem Comm. 2014, 50, 4853-4855. DOI:10.1039/C4CC01372G.

Fathalla, M.; Li, S.-C.; Neuberger, A. Schmehl, R.; Diebold, U.; Jayawickramarajah, J. Straightforward self-assembly of porphyrin nanowires in water: Harnessing adamantane/β-cyclodextrin interactions J. Am. Chem. Soc. 2010, 132, 9966-9967. DOI: 10.1021/ja1030722.

3. DNA-Small Molecule Chimeras (DCs) as Input Activated Protein Binders. We are developing novel DNA-small molecule chimeras (DCs) that serve as input-triggered protein binders/inhibitors. The generation of such novel inhibitor activation strategies is critical since traditional approaches to activate prodrugs are largely limited to covalent activation (e.g., enzyme or light mediated prodrug triggering). Since our strategy uses molecular recognition-based activation, it is possible to significantly expand the types of biomarkers (e.g., non-enzyme proteins, oligonucleotides, and small metabolites) that can be harnessed.

Representative Publications

Zhou, X.; Su, X.; Pathak, P.; Vik, R.; Vinciguerra, B.; Isaacs, L.; Jayawickramarajah, J. Host-Guest tethered DNA transducer: ATP fueled release of a protein inhibitor from cucurbit[7]uril. J. Am. Chem. Soc. 2017, 139, 13916-13921. DOI: 10.1021/jacs.7b07977.

Chu, X.; Battle, C.; Zhang, N.; Aryal, G. H.; Jayawickramarajah, J. Bile acid conjugated DNA chimera that conditionally inhibits carbonic anhydrase-II in the presence of microRNA-21. Bioconjugate Chemistry 2015, 26, 8,1601-1612. DOI:10.1021/acs.bioconjchem.5b00231.

Harris, D. C.; Saks, B. R.; Jayawickramarajah, J. Protein-binding molecular switches via host-guest stabilized DNA hairpins. J. Am. Chem. Soc. 2011, 133, 7676-7679. DOI: 10.1021/ja2017366.

Harris, D. C.; Chu, X; Jayawickramarajah, J. DNA-small molecule chimera with responsive protein-binding ability.

J. Am. Chem. Soc. 2008, 130, 14950-14951. DOI: 10.1021/ja806552c.

My research interests include the development and testing of semiclassical methods for systems involving transitions between molecular states and for systems where tunneling is important.  Semiclassical methods use information obtained from classical trajectories to provide a good approximation to the quantum mechanical description of molecular systems.

I am also using computer simulations to better understand the mechanisms for chain diffusion and stress relaxation in long chain polymer melts.  Of particular interest in these studies is elucidating the role of cooperative many chain motions.

A third area of current research aims at providing a better understanding of the propensities of different isotopes of an element to populate certain locations in a molecule.  In addition, a better understanding of how different isotopologues of a molecule, which have different isotopes at specific positions in the molecule, can alter phase equilibria.

Discipline

Physical Chemistry

Selected Publications

Azeotropic Isotopologues, R. P. Currier, T. B. Peery, M. F. Herman, R. Williams, R. Michalczyk, T. Larson, D. Labotka, J. Fessenden, and S. M. Clegg, Fluid Phase Equilibria, 493, 188-195(2018).

A Test of the Significance of Intermolecular Dipolar Vibrational Coupling in Isotopic Fractionation, M. F Herman, R, P. Currier, T. B. Peery, and S. M. Clegg, Chem. Phys. 494, 11-19 (2017).

Semiclassical Time Dependent Tunneling Using Real Trajectories, M. F. Herman, J. Chem. Phys. 143, 164110 (2015).

Surface Hopping, Transition State Theory and Decoherence 1: Scattering Theory and Time Reversibility, A. Jain, M. F. Herman, W. Ouyang, and J. E. Subotnik, J. Chem. Phys. 143, 134106 (2015).

Isotope Mass Effect on the Intermolecular Potential, M. F. Herman, R. P. Currier, and S. M. Clegg, Chem. Phys. Lett. 639, 266-268 (2015).

Analysis of a Surface Hopping Methods to Includes Hops in Classically Forbidden Regions, M. F. Herman, Chem. Phys. 433, 12 (2014).
 
Improving the Efficiency of Monte Carlo Surface Hopping Calculations, M. F. Herman, J. Phys. Chem. B. 118, 8026-8033 (2014).
 
A Justification for the Use of Approximate Transition Amplitudes in Semiclassical Surface, Phuong-Thanh  Dang and Michael F. Herman, Mol. Physics (2011)109(12) 1581-1592.

Erratum:  The Calculation of Multidimensional Semiclassical Wave Functions in the Forbidden Region Using Real Valued Coordinates, J. Chem. Phys. 134(8) 089901/1-089901/2.

Using Semiclassical Surface Hopping for Coupled Partial Wave Calculations on Systems with Non-Spherically Symmetric Potentials, M. F.
Herman, Chem. Phys. 373, 274-282 (2010).
 
The Calculation of Multidimensional Semiclassical Wave Functions in the Forbidden Region Using Real Valued Coordinates, M. F.  Herman, J. Chem. Phys. 133, 114108 (2010).

A Semiclassical Model for the Calculation of Nonadiabatic Transition Probabilities for Classically Forbidden Transitions, Phuong-Thanh
 Dang and Michael F. Herman, J. Chem. Phys. 130, 054107 (2009).
 
A Singularity Free Surface Hopping Expansion for the Multistate Wave Function, M. F. Herman, J. Chem. Phys. 131, 214108 (2009).
 
 MF Herman, Y Wu,  An Analysis Through Order   ℏ2 of a Surface Hopping Expansion of the Nonadiabatic Wave Function,  J. Chem. Phys., 128, 11405 (2008).

MF Herman, Higher Order Phase Corrected Transition Amplitudes for Time Dependent Semicalssical Surface Hopping Calculations, Chem Phys., 351, 51 (2008).

Affiliations:

• Bioinnovation 
• PolyRMC

Areas of current interest:

Macromolecular Architecture
The primary focus of the group involves control of nanoscale architecture through synthetic chemistry, focusing on tailoring nanomaterials towards application to real world problems. This can be carried out using a number of preparative tools, including traditional organic synthesis, polymer chemistry, dendrimer chemistry, and self-assembly—and most often a combination of two or more.

Material Applications
After decades of optimizing “top down” photolithographic patterning of polymer films for production of microelectronic devices, the existing process appears to be reaching fundamental limits. The ability to build structures in a “bottom up” fashion offers an attractive alternative to lithographic approaches but remains largely unexplored. By controlling the assembly of nanoscale materials through mechanisms such as DNA binding, hydrophobic/hydrophilic interactions, and electrostatic attraction, we hope to investigate new methodologies for building defined architectures on the 1-50 nm length scale. Incorporation of functional materials, such as organic conductors, nanocrystals, nanowires, and nantubes represent the long term goal for useful materials.

Medical Applications
The ability to control materials' nano-architecture also represents a useful tool for medical applications. For example, recent work has demonstrated that polymer drug conjugates offer selective uptake into cancer tissues offering a powerful passive targeting mechanism to greatly enhance the efficacy of drugs in cancer therapy. Similarly it is expected that the study and optimization of tailored macromolecules will yield useful vectors for a wide variety of medical treatments including gene, vaccine and drug delivery. Through collaborations with the Tulane medical school, nanomaterials will be designed, synthesized, and tested, in order to optimize their structure and probe their biological properties.

Discipline

Organic, Materials and Biochemistry

Our interdisciplinary research focuses on the development and study of novel supramolecular systems in aqueous solution. The aim of our work is two-fold. First, we seek to identify new and unique phenomena that can only arise though the precise structural control of nano-scale supramolecular species in solution. Examples include, the separation of hydrocarbon gases using aqueous solutions, selective molecular protection and the kinetic resolution of molecular mixtures, or the development of nano-scale reaction vessels. Second, we use supramolecular systems to study the fundamental properties of aqueous solutions, in particular the molecular basis of the Hydrophobic Effect and the Hofmeister Effect.

Discipline

Organic Chemistry

Selected Publications

http://www.gibbgroup.org/publications/selected-publications/

Areas of current interest:

• The synthesis of multiply-bonded silicon compounds, to study the effects of silicon p-conjugation related to the concepts of aromaticity and anti- aromaticity.
• Mechanistic investigations of transition-metal silicon chemistry, as it pertains to catalysis and materials synthesis.
• The study of organosilicon photochemistry and reactive intermediates, in fluid solution, inert matrices, and in molecular beams.
• The synthesis of novel precursors to technologically important ceramic fibers and thin films.

Discipline

Inorganic and Organometallic Chemistry

Dr. Fink's research interest in this area focuses primarily in the synthetic and mechanistic chemistry of silicon, boron and related elements.

Selected Publications

Pichaandi, K. R., Mague, J.T. and Fink, M.J. “Crystal Structures of Three Sterically Congested Disilanes”, Acta Cryst. E , 2017, 73 (3), 448-452.

Pichaandi, Kothanda Rama, Mague, J.T. and Fink, M.J. “Synthesis, Photochemical Decomposition and DFT studies of 2,2,3,3-Tetramethyl-1,1-bis(dimethylphenylsilyl) Silacyclopropane”, J. Organomet. Chem., 2015, 791, 163-168

Xu, Zejing; Li, Yejia; Zhang, Boyu ; Purkait, Tapas Alb, Alina; Mitchell, Brian S.; Grayson, Scott M. ; Fink, Mark J. “Water Soluble PEGylated Silicon Nanoparticles and Their Assembly into Swellable Nanoparticle Arrays” J. Nanoparticle Research, 2015, 17:56, DOI: 10.1007/s11051-015-2869-9

Mitchell, Brian S.; Wang, Hongqiang; Xu, Zejing; Fink, Mark J. ; Shchukin, Dmitry “Functionalized Photoluminescent Silicon Nanoparticles from Reactive Cavitation Erosion of Silicon Wafers”, Chem. Comm., 2015, 51, 1465-1467

Kuang, Li; Mitchell , Brian S.;, Fink , Mark J. “Silicon Nanoparticles Synthesized through Reactive High Energy Ball Milling: Enhancement of Optical Properties mfrom the Removal of Iron Impurities” J. of Exp. Nanoscience, 2014, 10, 16, 1214-1222, DOI: 10.1080/17458080.2014.989552

Xiaoye, Su ; Kuang, Li; Cooper, Battle; Ted, Shaner; Mitchell , Brian S. ; Fink, Mark J.; Jayawickramarajah, Janarthanan “A Mild Two-Step Method to Construct DNA-Conjugated Silicon Nanoparticles: Scaffolds for the Detection of MicroRNA-21” Bioconjug.Chem., 2014, 25, 1739-1743
 

Research in the Donahue Group is primarily synthesis-driven. Our research endeavors involve preparing new compounds as well as developing improved ways to access important types of molecules.

Discipline

Inorganic Chemistry

Selected Publications

https://www.donahuegroup.org/pubs

The primary research interest of our group is the mechanism of action of enzymes. Our recent work has focused on the hydrolytic enzymes, ß-glucosidase and hyaluronidase, and the glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase. In order to better understand the sources of the enormous catalytic efficiency, specificity and regulatory properties of enzymes we are making use of the classical probes of physical organic chemistry (e.g., structure-reactivity relationships and kinetic isotope effects). As a further probe of enzyme mechanisms we also make use of transition state analog inhibitors. These are stable compounds designed to resemble fleeting intermediates. Because of this resemblance they are bound by the enzyme much more tightly than are substrates. The more closely a transition state analog resembles the transition state the more tightly it should bind to the enzyme. Thus, we can get mechanistic information (i.e., transition state structure) by looking at reversible inhibitors.

The approach of using transition state analogs as enzyme inhibitors is useful not only in elucidating some of the structural features of the transition state but also as a basis for drug design. Indeed, there is an increasing number of drugs available which have been designed as transition state analogs for a variety of enzymes. Transition state analogs are also used in developing catalytic antibodies which can carry out reactions for which no known enzymes exist.

Area of current interest:

• Bio-Organic Chemistry

Selected Publications

K. Wang, X. Cai, W. Yao, D. Tang, R. Kataria, H.S. Ashbaugh, L.D. Byers and B.C. Gibb, “Electrostatic Control of Macrocyclization Reactions within Nanospaces” J. Am. Chem. Soc. 141, 6740-6747 (2019)

M. Xie and L.D. Byers, “Solvent and "-Secondary Kinetic Isotope Effects on β-Glucosidase” Biochim. Biophys. Acta 1854, 1776-1781 (2015)

E.A-B Avegno, G.S. Howarth, A. V. Demchenko and L.D. Byers, “Reactive Thioglucoside Substrates for β-Glucosidase” Arch. Biochem. Biophys. 537, 1-4 (2013)

Y Na, H Shen, Byers, LD, N-Phenylglucosylamine Hydrolysis:  A Mechanistic Probe of β-Glucosidase, Bioorganic Chemistry, 39, 111-113 (2011)

Alverson-Banks, E and Byers, LD, Multiple Inhibition of β-Glucosidase, Am Chem Soc (2011).

EG Golden and LD Byers, A Search for a Solvent Isotope Effect on a-Glucosidase, FASEB Journal (2008).

AH O'Donnell, X. Yao and LD Byers, Solvent Kinetic Isotope Effects on α-Glucosidase, Biochem. Biophys. Acta., 1703, 63 (2004).

EM Bowers, LO Ragland and LD Byers, Specific Ion Effects on β-Glucosidase, FASEB Journal, 18, C140 (2004).

EB Golden, AE O'Donnell and LD Byers, Solvent Isotope Effects on Binding to Glucosidases, FASEB Journal, 17, A983 (2003).

X. Yao, R. Mauldin and L. Byers, AMultiple Sugar Binding Sites in α-Glucosidase, Biochim. Biophys. Acta, 1645, 22 (2003).

L.O. Ragland and L.D. Byers,  Salt Effects on β-Glucosidase Kinetics, FASEB Journal 16, A535 (2002).

X. Yao, R. Mauldin and L. Byers, Multiple Sugar Binding Sites in Glucosidase, Biochim. Biophys. Acta, 1645, 22 (2003).

D. Nguyen and L. D. Byers, A α-Glucosidase Inhibition by Imidazoles, FASEB Journal 15, 1160 (2001).

My research interests include:

Development of transmembrane transporters
Membranes play an important biological function by avoiding the free movement of ions and polar molecules into the cell. The controlled transport of these compounds is regulated by specialized proteins (ion channels, efflux pumps, etc). However, in some cases these proteins malfunction (e.g. cystic fibrosis), or the barrier created by the membrane is problematic for drugs to reach their target. In our lab we therefore develop small molecules that can transport polar compounds such as ions, hydrophilic drugs and DNA/RNA across biological membranes.

Recognition of membrane components
The recognition of membrane components such as various types of phospholipids has been an underexplored field, even though membranes can have different compositions depending on the situation (e.g. bacterial cells consist of different lipids than mammalian cells, and cancer cells have different lipid ratios than healthy cells). We therefore aim to develop receptors that can recognize specific lipids in order to use them in medical applications.
 

Disciplines

Organic Chemistry, Supramolecular Chemistry, Medicinal Chemistry, Chemical Biology

Selected Publications

Busschaert, N., García-López, V., Ke, C., McGuirk, C.M., Shimizu, L.S., Gerthoffer, M.C., Bhattacharjee, N. NASC: Bringing Together Supramolecular Chemists from Across North America. Supramol. Chem. (2023). In Press. DOI: 10.1080/10610278.2023.2178724.

Herschede, S.R., Salam, R., Gneid, H., Busschaert, N. Bacterial cytological profiling identifies transmembrane anion transport as the mechanism of action for a urea-based antibiotic. Supramol. Chem. (2023). In Press. DOI: 10.1080/10610278.2023.2178921.

Leigh, J.S., Busschaert, N., Haynes, C.J., Hiscock, J.R., Hutchins, K.M., von Krbek, L.K., McConnell, A.J., Slater, A.G., Smith, D.K. and Draper, E.R. Planning a family. Nat. Rev. Chem., 6, 673–675 (2022). DOI: 10.1038/s41570-022-00427-0

Williams, E.S., Gneid, H., Marshall, S.R., González, M.J., Mandelbaum, J.A., Busschaert, N. A supramolecular host for phosphatidylglycerol (PG) lipids with antibacterial activity. Org. Biomol. Chem., 20, 5958-5966 (2022). DOI: 10.1039/D1OB02298A.

Slater, A., Caltagirone, C., Draper, E., Busschaert, N., Hutchins, K., Leigh, J. Pregnancy in the lab. Nat. Rev. Chem., 6, 163–164 (2022). DOI: 10.1038/s41570-022-00362-0

Leigh, J.S., Hiscock, J.R., Koops, S., McConnell, A.J., Haynes, C.J.E., Caltagirone, C., Kieffer, M., Draper, E.R., Slater, A.G., Hutchins, K.M., Watkins, D., Busschaert, N., von Krbek, L.K.S., Jolliffe, K.A., Hardie, M.J. Managing research throughout COVID-19: Lived experiences of supramolecular chemists. Chem, 8, 299-311 (2022). DOI: 10.1016/j.chempr.2022.01.001

Busschaert, N., Maity, D., Samanta, P.K., English, N.J., Hamilton, A.D. Improving structural stability and anticoagulant activity of a thrombin binding aptamer by aromatic modifications. ChemBioChem, 23, e2021006 (2022). DOI: 10.1002/cbic.202100670

Our research is in three areas of theoretical physical chemistry. The first area involves collaborative investigation of charge and exciton transport in DNA affected by the environment (solvent), charge-induced molecular reorganization and external laser or microwave fields. The second area involves optical energy transport, conversion and dissipation in inhomogeneous disordered or partially ordered arrays of nanoparticles. The third area deals with inhomogeneous kinetics and thermodynamics in amorphous solids and complex molecular systems.

Areas of current interest include:

• Complex Systems
• Optical Systems
• DNA-Photonics

Publications

2022

Xiaolong Deng, Alexander L. Burin, and IvanM Khaymovich. Anisotropy-mediated reentrant localization. SciPost Physics, 2022

Liuqi Yu, Shlomi Matityahu, Yaniv J. Rosen, Chih-Chiao Hung, Andrii Maksymov, Alexander L. Burin, Moshe Schechter, and Kevin D. Osborn. Experimentally revealing anomalously large dipoles in the dielectric of a quantum circuit. Scientific Reports, 12(1):16960, Oct 2022

Dilanka V. D. Walpita Kankanamalage, Jennifer H. T. Tran, Noah Beltrami, Kun Meng, Xiao Zhou, Pravin Pathak, Lyle Isaacs, Alexander L. Burin, Mehnaaz F. Ali, and Janarthanan Jayawickramarajah. Dna strand displacement driven by host–guest interactions. Journal of the American Chemical Society, 144(36):16502–16511, Sep 2022

Tammy X. Leong, Brenna K. Collins, Sourajit Dey Baksi, Robert T. Mackin, Artem Sribnyi, Alexander L. Burin, John A. Gladysz, and Igor V. Rubtsov. Tracking energy transfer across a platinum center. The Journal of Physical Chemistry A, 126(30):4915–4930, 2022. PMID: 35881911

Alexander L. Burin. Exact solution of the minimalist stark many-body localization problem in terms of spin-pair hopping. Phys. Rev. B, 105:184206,
May 2022

2021

Sithara U. Nawagamuwage, Layla N. Qasim, Xiao Zhou, Tammy X. Leong, Igor V. Parshin, Janarthanan Jayawickramarajah, Alexander L. Burin, and Igor V. Rubtsov. Competition of several energy-transport initiation mechanisms defines the ballistic transport speed. The Journal of Physical Chemistry B, 125(27):7546–7555, 2021. PMID: 34185993

Alexander Churkin, Shlomi Matityahu, Andrii O. Maksymov, Alexander L. Burin, and Moshe Schechter. Anomalous low-energy properties in amorphous solids and the interplay of electric and elastic interactions of tunneling two-level systems. Phys. Rev. B, 103:054202, Feb 2021

Ofek Asban, Alexander Burin, Alexander Shnirman, and Moshe Schechter. Polaronic effect of a metal layer on variable range hopping. Phys. Rev. B,
103:045129, Jan 2021

Alexander Churkin, Shlomi Matityahu, Andrii O. Maksymov, Alexander L. Burin, and Moshe Schechter. Anomalous low-energy properties in amorphous solids and the interplay of electric and elastic interactions of tunneling two-level systems. Phys. Rev. B, 103:054202, Feb 2021

2020

Alexei Boulatov and Alexander L. Burin. Crucial effect of transverse vibrations on the transport through polymer chains. The Journal of Chemical Physics, 153(13):134102, 2020

Robert T. Mackin, Tammy X. Leong, Natalia I. Rubtsova, Alexander L. Burin, and Igor V. Rubtsov. Low-temperature vibrational energy trans port via peg chains. The Journal of Physical Chemistry Letters, 11(12):4578–4583, 2020. PMID: 32437615

Andrii O. Maksymov and Alexander L. Burin. Many-body localization in spin chains with long-range transverse interactions: Scaling of critical disorder with system size. Phys. Rev. B, 101:024201, Jan 2020

2019

Alexander L. Burin, Andrii O. Maksymov, Ma’ayan Schmidt  and Il’ya Ya. Polishchuk, Chaotic Dynamics in a Quantum Fermi-Pasta-Ulam Problem, Entropy 2019, 21, 51; doi:10.3390/e21010051.

I. V. Rubtsov and A. L. Burin, Ballistic and diffusive vibrational energy transport in molecules, J. Chem. Phys. 150, 020901 (2019). 

Layla N. Qasim, E. Berk Atuk, Andrii O. Maksymov, Janarthanan Jayawickramarajah, Alexander L. Burin, and Igor V. Rubtsov. Ballistic transport of vibrational energy through an amide group bridging alkyl chains. The Journal of Physical Chemistry C, 123(6):3381–3392, 2019

2018
A.A. Anastasiev, A.L. Burin, M.I. Gozman, I. Ya. Polishchuk, Yu. I. Polishchuk, and E.A. Tsyvkunova, Guided modes in periodical arrays of waveguides, ICTON 2018, 978-1-5386-6605-0/18.

M. Schechter, P. Nalbach  and A. L. Burin, Nonuniversality and strongly interacting two-level systems in glasses at low temperatures, New J. Phys. 20 (2018) 063048.

Alexander L. Burin and Andrii O. Maksymov, Theory of nonlinear microwave absorption by interacting two-level systems, Phys. Rev. B 97, 214208 (2018).
 

2017
A. O. Maksymov, N. Rahman, E. Kapit, and A. L. Burin, Comment on “Many-body localization in Ising models with random long-range interactions,” Physical Review A 96 (2017) 057601.

N. Kirsh, E. Svetitsky, A. L. Burin, M. Schechter, N. Katz, Revealing the nonlinear response of a tunneling two-level system ensemble using coupled modes, Physical Review Materials 1 (2017), 012601 R.

I. V. Gornyi, A. D. Mirlin, D. G. Polyakov, A. L. Burin, Spectral diffusion and scaling of many-body delocalization transitions, Annalen der Physik 1600360 (2017), 1600360.

A.  L.  Burin, Localization and chaos in a quantum spin glass model in random longitudinal fields: Mapping to the localization problem in a Bethe lattice with a correlated disorder, Annalen der Physik 1600292 (2017), 1600292. Quoted by Advanced Science News, http://www.advancedsciencenews.com/localization-chaos-quantum-spin-glas… .

L. N. Qasim, A. Kurnosov, Y. K. Yue, Z. W. Lin, A. L. Burin, I. V. Rubtsov, Energy Transport in PEG Oligomers: Contributions of Different Optical Bands, Journal of Physical Chemistry C, v. 120, pp.  26663-26677 (2017).  
 

2016
A. A. Kurnosov, I. V. Rubtsov, A. O. Maksymov and A. L. Burin, Electronic torsional sound in linear atomic chains: Chemical energy transport at 1000 km/s, J. Chem. Phys. 145, 034903 (2016).

D.B. Gutman, I.V. Protopopov, A.L. Burin, I.V. Gornyi, R.A. Santos, A.D. Mirlin, Energy transport in the Anderson insulator, Phys. Rev. B 93, 245427 (2016).

B. Sarabi, A. N. Ramanayaka, A. L. Burin, F. C. Wellstood, and K. D. Osborn, Projected Dipole Moments of Individual Two-Level Defects Extracted Using Circuit Quantum Electrodynamics, Phys. Rev. Lett. 116, 167002 (2016).

Y. J. Rosen, M. S. Khalil, A. L. Burin, and K. D. Osborn, The tunneling atom laser: Manipulating lossy two-level defects to produce a circuit with coherent gain, Phys. Rev. Lett. 116, 163601 (2016).
 

2015
B. Sarabi, A. N. Ramanayaka, A. L. Burin, F. C. Wellstood and K. D. Osborn, Cavity quantum electrodynamics using a near-resonance two-level system: Emergence of the Glauber state, Appl. Phys. Lett. 106, 172601 (2015, featured article).

N. I. Rubtsova, C. M. Nyby, H. Zhang, B. Zhang, X. Zhou, J. Jayawickramarajah, A. L. Burin and I. V. Rubtsov, Room-temperature ballistic energy transport in molecules with repeating units, J. Chem. Phys. 142, 212412 (2015).

A.L. Burin, Many-body delocalization in a strong disorderly system with long-range interactions: Finite-size scaling, Phys. Rev. B 91, 094202 (2015).

B. Sarabi. A. N. Ramanayaka, A. L. Burin, F. C. Wellstood, K. D. Osborn, Cavity quantum electrodynamics of nanoscale two-level systems, arXiv:1405.0264 [cond-mat.supr-con], Submitted to Phys. Rev. Lett.

 A. A. Kurnosov, I. V. Rubtsov and A. L. Burin, Communication: Fast transport and relaxation of vibrational energy in polymer chains, J. Chem. Phys. 142, 011101 (2015).
 

2014
M. S. Khalil, S. Gladchenko, M. J. A. Stoutimore, F. C. Wellstood, A. L. Burin, and K. D. Osborn, Landau-Zener population control and dipole measurement of a two-level-system bath, Phys. Rev. B 90, 100201(R)

A. L. Burin, A. O. Maksymov, K. D. Osborn, Quantum coherent manipulation of two-level systems in superconducting circuits, Superconducting Science and Technology, 27 (2014) 0804001.

N. I. Rubtsova, A. K. Kurnosov, A. L. Burin, I. V. Rubtsov, Temperature dependence of the ballistic energy transport in perfluoroalkanes, J. Phys. Chem. B 18 (28), pp 8381–8387 (2014).
 

2013
S. L. Tesar, V. M. Kasyanenko, I. V. Rubtsov, G. I. Rubtsov, A. L. Burin, Theoretical Study of Internal Vibrational Relaxation and Energy Transport in Polyatomic Molecules, J. Phys. Chem. A 117, 2, 315-323 (2013).

 A. L. Burin, J. M. Leveritt Jr., G. Fickenscher, A. Fleischmann, C. C. Enss, C. Schoetz, M. Bazrafshan, P. Fasl and M. v. Schickfus, Low temperature dipolar echo in amorphous dielectrics: Significance of relaxation and decoherence free two level systems, Euro Physics Letters, 104 (2013) 57006.

 A. L. Burin, M. S. Khalil, K. D. Osborn, Universal dielectric loss in amorphous solids from simultaneous bias and microwave field, Physical Review Letters 110, 157002 (2013).
 

2012
A. L. Burin, J. M. Leveritt Jr., G. Fickenscher, A. Fleischmann, C. C. Enss, C. Schoetz, M. Bazrafshan, P. Fasl and M. v. Schickfus, Low temperature dipolar echo in amorphous dielectrics: Significance of relaxation and decoherence free two level systems, Preprint, arXiv:1208.2883v1 [cond-mat.dis-nn], http://arxiv.org/pdf/1208.2883v1.pdf.

A. L. Burin, M. S. Khalil, K. D. Osborn, Universal dielectric loss in amorphous solids from simultaneous bias and microwave field. Preprint, arXiv:1205.4982v1 [cond-mat.dis-nn], http://arxiv.org/pdf/1205.4982v1.pdf.

A. L. Burin, A. K. Kurnosov, Fluctuator model of memory dip in hopping insulators, J. Low Temp. Phys., 167, 318-328 (2012).

Sarah L. Tesar, John M. Leveritt III, Arkady A. Kurnosov, Alexander L. Burin, Temperature dependence for the rate of hole transfer in DNA: Nonadiabatic regime, Chemical Physics 393 (2012) 13–18.
 

2011
A. L. Burin, A. K. Kurnosov, Fluctuator model of memory dip in hopping insulators, European Superconductivity News Forum, CR25 (http://www.ewh.ieee.org/tc/csc/europe/newsforum/pdf/CR25.pdf) (2011).

V. M. Kasyanenko, S. L. Tesar, G. I. Rubtsov, A. L. Burin, I. V. Rubtsov, Structure Dependent Energy Transport: Relaxation-Assisted 2DIR Measurements and Theoretical Studies, J. Phys. Chem. B 115,  pp. 11063-11073 (2011).
 

2010
A. L. Burin, S. L. Tesar, V. M. Kasyanenko, I. V. Rubtsov, G. I. Rubtsov, Semiclassical Model for Vibrational Dynamics in Polyatomic Molecules: Investigation of Internal Vibrational Relaxation, J. Phys. Chem. C, 2010, 114 (48), pp 20510–20517.

S. M. Mickley Conron, A. K. Thazhathveetil, M. R. Wasielewski, A. L. Burin, and F. D. Lewis, Direct Measurement of the Dynamics of Hole Hopping in Extended DNA G-Tracts. An Unbiased Random Walk J. Am. Chem. Soc., 132 (41), pp. 14388–14390 (2010).

G. S. Blaustein, F. D. Lewis, A. L. Burin, Kinetics of Charge Separation in Poly(A)-Poly(T) DNA Hairpins , J. Phys. Chem. 114, pp. 6732-6739 (2010).

I. Ya. Polishchuk, M. I. Gozman, G. S. Blaustein, A. L. Burin,  Interference of guided modes in a two-port ring waveguide composed of dielectric nanoparticles, Phys. Rev. E 81, 026601 (2010).
 

2009
J. M. Leveritt III, C. Dibaya, S. Tesar, R. Shrestha, A. L. Burin, One dimensional confinement of electric field and humidity dependent DNA conductivity, Journal of Chemical Physics 131, 245102 (2009).

G. S. Blaustein, F. D. Lewis, A. L. Burin, R. Shrestha, The kinetics of charge recombination in DNA hairpins, controlled by counterions, International Conference on Computational Science 2009, Part II, LNCS 5545, pp. 189-196, Springer-Verlag Berlin Heidelberg,189–196, Eds:  G. Allen, J. Nabrzyski, Ed Seidel.

A. L. Burin, M. E. Armbruster, M. Hariharan, and F. D. Lewis, Sum rules and determination of exciton coupling using absorption and circular dichroism spectra of biological polymers, Proceedings of the National Academy of Science  106 (4) 989–994 (2009).

G. S. Blaustein, B. Demas, F. D. Lewis, and A. L. Burin, Charge Recombination in DNA Hairpins Controlled by Counterions, Journal of the American Chemical Society (Communications) 131 (2), 400-401 (2009).
 

2008
A. L. Burin,  J. A. Dickman, D. B. Uskov, C. F. F. Hebbard, G. C. Schatz, Optical absorption spectra and monomer interaction in polymers: Investigation of exciton coupling in DNA hairpins, Journal of Chemical Physics 129, 091102 (2008).

A. L. Burin,  J. A. Dickman, D. B. Uskov, C. F. F. Hebbard, G. C. Schatz, Optical absorption spectra and monomer interaction in polymers: Investigation of exciton coupling in DNA hairpins, Journal of Chemical Physics 129, 091102 (2008).

D. B. Uskov, A. L. Burin, Strong localization of positive charge in DNA from a charge-balance theory, Physical Review B 78, 073106 (2008).

A. L. Burin, D. B. Uskov, Strong localization of positive charge in DNA induced by its interaction with environment, Journal of Chemical Physics 129, 025101 (2008).

M. I. Gozman, I. Ya. Polishchuk, A. L. Burin, Light propagation in linear arrays of spherical particles, Physics Letters A 372, 5250–5253 (2008).

I. S. Tupitsyn, P. C. E. Stamp, A. L. Burin, Stability of Bose-Einstein Condensates of Hot Magnons in Yttrium Iron Garnet Films, Physical Review Letters 100, 257202 (2008).

A. L. Burin, V. I. Kozub, Y. M. Galperin, and V. Vinokur, Slow relaxation of conductance of amorphous hopping insulators, J. Phys. Condens. Matter 20, 244135 (2008).

A. L. Burin, B. I. Shklovskii, V. I. Kozub, Y. M. Galperin, and V. Vinokur, Many electron theory of 1/f noise in hopping conductivity, Invited Article, Phys. Stat. Sol. 5, 800-808 (2008)

Dr. Wang holds an appointment in the department of Ophthalmology at Tulane. His research interests include dissecting the epigenetic mechanisms of retinal vascular development and disease using genetic mouse model and in vitro system, with a focus on microRNAs and chromatin factors. The long term goal of his research is to develop novel and effective therapeutics for degenerative eye diseases.