The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke “design creationism” to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane’s hydrophobic/philic nature; a selective “pore” for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the “jackprot,” which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation http://faculty.rwu.edu/cbai/JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the “jackprot,” or highest-fitness complete-peptide sequence, required cumulative smaller “wins” (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (“jackdons” that led to “jackacids” that led to the “jackprot”). The “jackprot” is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide “edition” and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists

Impurity scattering and Friedel oscillations in mono-layer black phosphorus

We study the effect of impurity scattering effect in black phosphorurene (BP) in this work. For single impurity, we calculate impurity induced local density of states (LDOS) in momentum space numerically based on tight-binding Hamiltonian. In real space, we calculate LDOS and Friedel oscillation analytically. LDOS shows strong anisotropy in BP. Many impurities in BP are investigated using $T$-matrix approximation when the density is low. Midgap states appear in band gap with peaks in DOS. The peaks of midgap states are dependent on impurity potential. For finite positive potential, the impurity tends to bind negative charge carriers and vise versa. The infinite impurity potential problem is related to chiral symmetry in BP

Searching for high-KK isomers in the proton-rich A∼80A\sim80 mass region

Configuration-constrained potential-energy-surface calculations have been performed to investigate the $K$ isomerism in the proton-rich $A\sim80$ mass region. An abundance of high-$K$ states are predicted. These high-$K$ states arise from two and four-quasi-particle excitations, with $K^{\pi}=8^{+}$ and $K^{\pi}=16^{+}$, respectively. Their excitation energies are comparatively low, making them good candidates for long-lived isomers. Since most nuclei under studies are prolate spheroids in their ground states, the oblate shapes of the predicted high-$K$ states may indicate a combination of $K$ isomerism and shape isomerism

Quasi-particle random phase approximation with quasi-particle-vibration coupling: application to the Gamow-Teller response of the superfluid nucleus 120^{120}Sn

We propose a self-consistent quasi-particle random phase approximation (QRPA) plus quasi-particle-vibration coupling (QPVC) model with Skyrme interactions to describe the width and the line shape of giant resonances in open-shell nuclei, in which the effect of superfluidity should be taken into account in both the ground state and the excited states. We apply the new model to the Gamow-Teller resonance in the superfluid nucleus $^{120}$Sn, including both the isoscalar spin-triplet and the isovector spin-singlet pairing interactions. The strength distribution in $^{120}$Sn is well reproduced and the underlying microscopic mechanisms, related to QPVC and also to isoscalar pairing, are analyzed in detail.Comment: 32 pages, 11 figures, 4 table

Fiber Based Multiple-Access Optical Frequency Dissemination

We demonstrate a fiber based multiple-access optical frequency dissemination scheme. Without using any additional laser sources, we reproduce the stable disseminated frequency at an arbitrary point of fiber link. Relative frequency stability of 3E10^{-16}/s and 4E10^{-18}/10^4s is obtained. A branching fiber network for highly-precision synchronization of optical frequency is made possible by this method and its applications are discussed.Comment: 5 pages, 3 figure