In modern fundamental theories, there often is consideration of higher dimensions, often in the context of what can be written as a Schrödinger equation. Thus, the energetics of bound states in different dimensions is of interest. By considering the quantum square well in continuous D dimensions, it is shown that there is always a bound state for 0 < D ≤ 2. This binding is complete for D → 0 an...

We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After demonstrating our approach on two reaction rate problems, we present a biophysical model that describes how proteins evolve new functions while maintaining thermody...

It has been proposed that the annihilation process νν → ee → γγ may be responsible for the generation of gamma-ray bursts (GRBs). The incipient neutrino–antineutrino pairs carry virtually all of the gravitational binding energy available from the central engine. However, gamma-ray bursters proposed to date are inevitably surrounded by an excess of baryons, leading to the “baryon-loading problem...

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...

Electronic spectra are reported for the metal cluster (Tef) and metal cluster complex (Ag+-benzene, Mg'-C02) cations. These ions are generated by laser vaporization in a pulsed nozzle source, jet-cooled, mass-selected with a reflectron time-of-flight spectrometer, and dissociated on resonance with a tunable dye laser. Electronic excitation spectra are recorded by monitoring the appearance of th...

SUMMARY Macromolecular assembly coordinates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential increase of the number of configurational states with the number of components. CplexA is a Mathematica package that uses functional programming to efficiently comp...

Electronic structure calculations on million-atom samples are employed to investigate the effect of macroscopic deformations on energetics of vacancies in aluminum. We find that volumetric strain associated with a deformation largely governs the formation energies of monovacancies and divacancies. The calculations suggest that nucleation of these defects is increasingly favorable under volumetr...

Histone deacetylases (HDACs) have emerged as important drug targets in epigenetics. The most common HDAC inhibitors use hydroxamic acids as zinc binding groups despite unfavorable pharmacokinetic properties. A two-stage protocol of M05-2X calculations of a library of 48 fragments in a small model active site, followed by QM/MM hybrid calculations of the full enzyme with selected binders, is use...