Cellular properties and population asymptotics in the population balance equation

Proliferating cell populations at steady-state growth often exhibit broad protein distributions with exponential tails. The sources of this variation and its universality are of much theoretical interest. Here we address the problem by asymptotic analysis of the population balance equation. We show that the steady-state distribution tail is determined by a combination of protein production and cell division and is insensitive to other model details. Under general conditions this tail is exponential with a dependence on parameters consistent with experiment. We discuss the conditions for this effect to be dominant over other sources of variation and the relation to experiments.     

Theory of three-dimensional alignment by intense laser pulses

We introduce a theoretical framework for study of three-dimensional alignment by moderately intense laser pulses and discuss it at an elementary level. Several features of formal interest are noted and clarified. Our approach is nonperturbative, treating the laser field within classical and the material system within quantum mechanics. The theory is implemented numerically using a basis set of rotational eigenstates, transforming the time-dependent Schrodinger equation to a set of coupled differential equations where all matrix elements are analytically soluble. The approach was applied over the past few years to explore different adiabatic and nonadiabatic three-dimensional alignment approaches in conjunction with experiments, but its formal details and numerical implementation were not reported in previous studies. Although we provide simple numerical examples to illustrate the content of the equations, our main goal is to complement previous reports through an introductory discussion of the underlying theory.     

Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization

The nucleotidyl-transfer reaction coupled with the conformational transitions in DNA polymerases is critical for maintaining the fidelity and efficiency of DNA synthesis. We examine here the possible reaction pathways of a Y-family DNA polymerase, Sulfolobus solfataricus DNA polymerase IV (Dpo4), for the correct insertion of dCTP opposite 8-oxoguanine using the quantum mechanics/molecular mechanics (QM/MM) approach, both from a chemistry-competent state and a crystal closed state. The latter examination is important for understanding pre-chemistry barriers to interpret the entire enzyme mechanism, since the crystal closed state is not an ideal state for initiating the chemical reaction. The most favorable reaction path involves initial deprotonation of O3'H via two bridging water molecules to O1A, overcoming an overall potential energy barrier of approximately 20.0 kcal/mol. The proton on O1A-P(alpha) then migrates to the gamma-phosphate oxygen of the incoming nucleotide as O3' attacks P(alpha), and the P(alpha)-O3A bond breaks. The other possible pathway in which the O3'H proton is transferred directly to O1A on P(alpha) has an overall energy barrier of 25.0 kcal/mol. In both reaction paths, the rate-limiting step is the initial deprotonation, and the trigonal-bipyramidal configuration for P(alpha) occurs during the concerted bond formation (O3'-P(alpha)) and breaking (P(alpha)-O3A), indicating the associative nature of the chemical reaction. In contrast, the Dpo4/DNA complex with an imperfect active-site geometry corresponding to the crystal state must overcome a much higher activation energy barrier (29.0 kcal/mol) to achieve a tightly organized site due to hindered O3'H deprotonation stemming from larger distances and distorted conformation of the proton acceptors. This significant difference demonstrates that the pre-chemistry reorganization in Dpo4 costs approximately 4.0 to 9.0 kcal/mol depending on the primer terminus environment. Compared to the higher fidelity DNA polymerase beta from the X-family, Dpo4 has a higher chemical reaction barrier (20.0 vs 15.0 kcal/mol) due to the more solvent-exposed active site.     

Optimal design of nanoplasmonic materials using genetic algorithms as a multiparameter optimization tool

An optimal control approach based on multiple parameter genetic algorithms is applied to the design of plasmonic nanoconstructs with predetermined optical properties and functionalities. We first develop nanoscale metallic lenses that focus an incident plane wave onto a prespecified, spatially confined spot. Our results illustrate the mechanism of energy flow through wires and cavities. Next we design a periodic array of silver particles to modify the polarization of an incident, linearly polarized plane wave in a desired fashion while localizing the light in space. The results provide insight into the structural features that determine the birefringence properties of metal nanoparticles and their arrays. Of the variety of potential applications that may be envisioned, we note the design of nanoscale light sources with controllable coherence and polarization properties that could serve for coherent control of molecular, electronic, or electromechanical dynamics in the nanoscale.     

Substitution-Inert Metal Complex Mobile Phases in Non-Suppressed Cation Chromatography

Substitution-inert metal complexes, [Co(edda)(H₂O)₂]⁺, (Co(edda)(en)]⁺, [Co(edda)(dmen)]⁺, [Co(en)₂-(gly)]²⁺, [Co(en)₂(acac)]²⁺, and [Co(trien)(gly)]²⁺ in their nitrate salt solutions are used as eluents in nonsuppressed cation chromatography (where edda = ethylenediamine-N,N′-diacetic acid, en = ethylenediamine, dmen = N,N′-dime-thylethylenediamine, gly = glycine, acac = acetylacetone, and trien = triethylenetetraamine). It is found that all the mono- and di-valent charged complexes can be used to separate alkali and alkaline earth metal cations, respectively. The separations for monovalent cations are sometimes comparable to those using ultrapure HNO₃ solutions. However, the divalent Ca²⁺ and Sr²⁺ ions cannot be resolved using the metal complex eluents. On the other hand, a selected, direct non-suppressed IC separation of zinc(II) and cadmium(II) ions is demonstrated for the first time using a substitution-inert metal complex eluent and a conductivity detector. Comparisons of these eluents with those reported previously, i. e. HNO₃ and ethylenediammonium salt solution are made and explanations are proposed to account for the different selectivities observed where possible. The future development of this technique is also briefly discussed.     

Astrophysical neutrinos: flavor ratios depend on energy

Electromagnetic (and adiabatic) energy losses of pi's and mu's modify the flavor ratio (measured at Earth) of neutrinos produced by pi decay in astrophysical sources, Phi v: phi v mu: phi v tau, from 1:1:1 at low energy to 1:1.8:1.8 at high energy. The transition occurs over 1-2 decades of v energy, and is correlated with a modification of the neutrino spectrum. For gamma-ray bursts, e.g., the transition is expected at approximately 100 TeV and may be detected by km-scale v telescopes. Measurements of the transition energy and energy width will provide unique probes of the physics of the sources. Pi and mu energy losses also affect the ratio of ve flux to total v flux, which may be measured at the resonance (6.3 PeV): It is modified from 1/6(1/15) at low energy to 1/9 (practically 0) at high energy for neutrinos produced in p p (p gamma) interactions.