Microarrays with biomolecules (e.g., DNA and proteins), cells, and tissues immobilized on solid substrates are important tools for biological research, including genomics, proteomics, and cell analysis. In this paper, the current state of microarray fabrication is reviewed. According to spot formation techniques, methods are categorized as "contact printing" and "non-contact printing." Contact ...

In constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approa...

We have studied single-stranded DNA translocation through a semiconductor membrane consisting of doped p and n layers of Si forming a p-n-junction. Using Brownian dynamics simulations of the biomolecule in the self-consistent membrane-electrolyte potential obtained from the Poisson-Nernst-Planck model, we show that while polymer length is extended more than when its motion is constricted only b...

Introduction Stimuli-responsive gels undergo abrupt changes in volume in response to environmental changes such as pH and temperature. Stimuli-responsive gels have attracted considerable attention as smart materials in the biochemical and biomedical fields, since they can sense environmental changes and induce structural changes by themselves. The fascinating properties of such stimuli-responsi...

Clathrate hydrates form the basis of a general model of biomolecule hydration. In clathrate hydrate crystal structures, the size of hydrogen-bonded water rings is highly constrained to five members. The clathrate hydrate model predicts that the size of water rings near biomolecule surfaces is similarly constrained to five members. This report describes a test of this model of biomolecule hydrat...

Biopolymers such as proteins and nucleic acids can be labeled with a fluorescent marker to allow for their detection. Covalent labeling is achieved by the reaction of an appropriately functionalized dye marker with a reactive group on a biomolecule. The recent trend, however, is the use of noncovalent labeling that results from strong hydrophobic and/or ionic interactions between the marker and...

We report on a new sensor strategy that we have termed protein imprinted xerogels with integrated emission sites (PIXIES). The PIXIES platform is completely self-contained, and it achieves analyte recognition without a biorecognition element (e.g., antibody). The PIXIES relies upon sol-gel-derived xerogels, molecular imprinting, and the selective installation of a luminescent reporter molecule ...

This thesis presents a set of numerical techniques that extend and improve computational modeling approaches for biomolecule analysis and design. The presented research focuses on surface formulations of modeling problems related to the estimation of the energetic cost to transfer a biomolecule from the gas phase to aqueous solution. The thesis discusses four contributions to modeling biomolecu...

BACKGROUND Fourier-transform infrared (FT-IR) spectrometry has been used to measure small molecules in plasma. We wished to extend this use to measurement of plasma proteins. METHODS We analyzed plasma proteins, glucose, lactate, and urea in 49 blood samples from 35 healthy subjects and 14 patients. For determining the concentration of each biomolecule, the method used the following steps: (a...