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20 Aug 2012

Volume 101, Issue 8, Articles (08xxxx)

Issue Cover Spotlight Figure

Appl. Phys. Lett. 101, 081102 (2012); http://dx.doi.org/10.1063/1.4745791 (3 pages)

M. K. Wu, M. Feng, and N. Holonyak, Jr.
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Dipole entropy based techniques for segmentation of introns and exons in DNA

Nithya Ramakrishnan and R. Bose

Appl. Phys. Lett. 101, 083701 (2012); http://dx.doi.org/10.1063/1.4747205 (4 pages)

Online Publication Date: 20 August 2012

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We have used superinformation, which is a measure of the disorder of the entropy content of different portions of a sequence, to analyze the structural variations of the introns and exons in DNA. We have computed superinformation for the angles of the dipole moments of the base-pairs and nucleotides in the double and single-stranded forms of DNA, respectively. We show that the computed dipole-angular superinformation of the introns are significantly higher than those of the exons and that these techniques could be used for intron-exon segmentation. They also yield more accurate and computationally faster results than the previously reported methods.
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87.14.gk DNA
87.15.B- Structure of biomolecules
87.15.Qt Sequence analysis
36.20.Fz Constitution (chains and sequences)

Molecular mechanics of dihydroxyphenylalanine at a silica interface

Zhao Qin and Markus Buehler

Appl. Phys. Lett. 101, 083702 (2012); http://dx.doi.org/10.1063/1.4747214 (4 pages) | Cited 1 time

Online Publication Date: 20 August 2012

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L-3,4-dihydroxyphenylalanine (DOPA) is an amazing biological glue secreted by marine mussels. Through enhanced sampling molecular dynamics, here we demonstrate that proteins with DOPA residues have a strong affinity to a silica surface with an interfacial strength of several hundreds of thousand N/cm2. The mechanism of such strong adhesion is a pair of hydrogen bonds that forms between DOPA and the substrate, enabling enhanced cooperativity as the DOPA residue lays flat on top the surface. Our predicted adhesion force (743 pN) agrees well with experimental measurements (847 ± 157 pN), including the orientation of the DOPA residue on the surface.
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87.15.ap Molecular dynamics simulation
87.15.B- Structure of biomolecules
87.15.H- Dynamics of biomolecules
36.20.Ey Conformation (statistics and dynamics)
36.20.Hb Configuration (bonds, dimensions)
87.14.E- Proteins

Laser-induced photo-thermal magnetic imaging

David A. Thayer, Yuting Lin, Alex Luk, and Gultekin Gulsen

Appl. Phys. Lett. 101, 083703 (2012); http://dx.doi.org/10.1063/1.4742158 (5 pages)

Online Publication Date: 23 August 2012

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Due to the strong scattering nature of biological tissue, optical imaging beyond the diffusion limit suffers from low spatial resolution. In this letter, we present an imaging technique, laser-induced photo-thermal magnetic imaging (PMI), which uses laser illumination to induce temperature increase in a medium and magnetic resonance imaging to map the spatially varying temperature, which is proportional to absorbed energy. This technique can provide high-resolution images of optical absorption and can potentially be used for small animal as well as breast cancer and lymph node imaging. First, we describe the theory of PMI, including the modeling of light propagation and heat transfer in tissue. We also present experimental data with corresponding predictions from theoretical models, which show excellent agreement.
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87.63.lt Laser imaging
42.62.Be Biological and medical applications
87.19.Pp Biothermics and thermal processes in biology
87.61.-c Magnetic resonance imaging
87.19.xj Cancer
87.63.L- Visual imaging
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