24,872 research outputs found
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 ādesign creationismā 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 membraneās hydrophobic/philic nature; a selective āporeā 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 ājackprot,ā 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 ājackprot,ā or highest-fitness complete-peptide sequence, required cumulative smaller āwinsā (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (ājackdonsā that led to ājackacidsā that led to the ājackprotā). The ājackprotā 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 āeditionā 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 -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- isomers in the proton-rich mass region
Configuration-constrained potential-energy-surface calculations have been
performed to investigate the isomerism in the proton-rich mass
region. An abundance of high- states are predicted. These high- states
arise from two and four-quasi-particle excitations, with and
, 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- states may indicate a combination of isomerism
and shape isomerism
Quasi-particle random phase approximation with quasi-particle-vibration coupling: application to the Gamow-Teller response of the superfluid nucleus 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 Sn, including both the isoscalar
spin-triplet and the isovector spin-singlet pairing interactions. The strength
distribution in 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
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