Generation of nanomechanical cantilever motion from biomolecular interactions can have wide applications, ranging from high-throughput biomolecular detection to bioactuation. Although it has been suggested that such motion is caused by changes in surface stress of a cantilever beam, the origin of the surface-stress change has so far not been elucidated. By using DNA hybridization experiments, w...

Non-normality can underlie pulse dynamics in many engineering contexts. However, its role in pulses generated in biomolecular contexts is generally unclear. Here, we address this issue using the mathematical tools of linear algebra and systems theory on simple computational models of biomolecular circuits. We find that nonnormality is present in standard models of feedforward loops. We used a g...

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substra...

Nanomaterials have been used extensively in the development of high sensitivity and high selectivity biodetection schemes. Designer particles, including noble-metal polyhedral structures, quantum dots, nanopatterns, and nanorods have found application in many forms of biological tagging schemes, including DNA and protein detection, cell sorting, and histochemical staining. Significant advantage...

In biomolecular simulations intensive computations are spent in nonbonded interactions kernels, i.e., electrostatic interactions. Therefore this part can be considered as a bottleneck, and its optimization permits biomolecular simulation methods to deal with more complex systems or to simulate longer time scales. Using novel computational architectures, i.e., the Cell processor, and programming...

The complexity of biomolecular interactions and influences is a major obstacle to their comprehension and elucidation. Visualizing knowledge of biomolecular interactions increases comprehension and facilitates the development of new hypotheses. The rapidly changing landscape of high-content experimental results also presents a challenge for the maintenance of comprehensive knowledgebases. Distr...

In the context of the macroscopic quantum phenomena of the second kind, we hereby seek for a solution-in-principle of the long standing problem of the polymer folding, which was considered by Levinthal as (semi)classically intractable. To illuminate it, we applied quantum-chemical and quantum decoherence approaches to conformational transitions. Our analyses imply the existence of novel macrosc...