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054950a8d17dab8f997c969f81c3525b5c5d3312 | subsection | 11 | 19 | Equilibrium eccentricity | The body is not disrupted if
\sqrt{2Q_{\rm D}}/v_{\rm K} > e_{\rm drag}, which
is equivalent to\begin{array}{l}
M M_{\rm mat} \simeq 0.8 \times 10^{-17} f_g^{-1.9}
\left(\frac{\gamma }{10^{-3}}\right)^{-3.7}
\left(\frac{\rho _{\rm p}}{3{\rm gcm}^{-3}}\right)^{-0.9}
\left(\frac{r}{1{\rm AU}}\right)^{2.8} M_{\oplus },
\... | {
"cite_spans": []
} | 10.1086/591903 | 0807.1761 | Accretion and destruction of planetesimals in turbulent disks | [
"Shigeru Ida",
"Tristan Guillot",
"Alessandro Morbidelli"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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07dcd7b9c98c9f4498bcabede045d76ff232ff58 | subsection | 12 | 19 | Accretion/destruction of planetesimals in an evolving disk | We now put these various critical physical radii in the context of the
evolution of the protoplanetary disk. In order to investigate the
effect of departures from power-law relations of the surface density
and temperature profiles in real disks, we also present in this section
results obtained from a 1D disk model that... | {
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adbc2696118b37262993b1d64dbb9ed18400a2f8 | subsection | 13 | 19 | Accretion/destruction of planetesimals in an evolving disk | Although the original MMSN model by used
r_{\rm edge} = 35 AU,
we here adopt r_{\rm edge} = 1000 AU
(for comparison, our fiducial alpha disk model with T_{\rm atm}=100 K
extends up to a maximum of 350 AU).These are found to be in excellent agreement with the analytical
expressions
derived in the previous section, with ... | {
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03c7466d3ddcb280f9050a6afe1c99b130c98a1c | subsection | 14 | 19 | Accretion/destruction of planetesimals in an evolving disk | The disk mass necessary for Jupiter to grow to its present mass
if it captures 70% of the mass flux at its orbital distance. For
our model, M_{\rm disk}=0.0054\,\rm M_\odot (about 5 times the
mass of Jupiter) and an age of 2.85 Myrs.Table REF provides the values of the physical
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bfd75edf6a6123322faf32995846338f8382b81f | subsection | 15 | 19 | Conclusion and discussion | We have investigated the critical physical radii for collisions between
planetesimals to be accretional (R > R_{\rm acc})
or disruptive (R < R_{\rm dis}) in turbulent disks,
as functions of turbulent strength
(\gamma \sim O(\Delta \rho /\rho )),
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336af8532373fdbabd27d2615600f342f38cbe30 | subsection | 16 | 19 | Conclusion and discussion | The
possibility to delay planet formation while keeping non-migrating
km-size planetesimals is noteworthy because it would help planetary
systems resisting to type-I migration: they would grow in a gas disk
that is less dense, and for which migration timescales may be
considerably increased. , , and
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"Shigeru Ida",
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ce05cb39914e2ca721fab6ebcaba9c0e3096f6df | subsection | 17 | 19 | Conclusion and discussion | This is in qualitative agreement with observations that do
not indicate a significant depletion of micron-sized grains with time,
contrary to what would be predicted in the absence of turbulence
, .In conclusion, the existence of MRI turbulence may be a threat to
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f2b16567b7ef282558ac90297f54c7d1197c6fda | subsection | 18 | 19 | Appendix | Here we derive the r-dependence in eq. (REF ).
If the equation of motion is scaled by a reference radius r_1
and T_{\rm K1} where T_{\rm K1} is a Keplerian period at r_1,
the only remaining non-dimensional parameter in the equations is\gamma \Gamma (r_1) = \gamma \frac{64 \Sigma _g r^2}{\pi M_{\odot }}|_{r_1}(see eqs. ... | {
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b38e48ed967f63f7faa04ff624e43d0153697440 | abstract | 0 | 28 | Abstract | There is an intrinsic relationship between the molecular evolution in
primordial period and the properties of genomes and proteomes of contemporary
species. The genomic data may help us understand the driving force of evolution
of life at molecular level. In absence of evidence, numerous problems in
molecular evolution... | {
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} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
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b68a5c52cfd17f75be31ea7f1e9b91c5596b5c88 | subsection | 1 | 28 | Introduction | The driving force of evolution of life is a core problem in the
theory of evolution. A qualified mechanism on driving force should
explain the evolutionary trends for both molecular evolution and
macroevolution of life. The driving force must be effective
persistently from the primordial period through present days. An... | {
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4b99df5365330f10c8d1c57961af25914e1c94c3 | subsection | 2 | 28 | Choosing orders of species properly to observe
variation trends of amino acid frequencies | The amino acid frequencies in species vary slightly, which was
routinely assumed to be constant . Unfortunately, this is a misleading assumption and
resulted in ignorance of studying the mechanism of variation of
amino acid frequencies in the past. Actually, it is easy to observe
the variation trends of amino acid freq... | {
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94602473f54bc43099b6a99ed420d8edba215ce4 | subsection | 3 | 28 | Choosing orders of species properly to observe
variation trends of amino acid frequencies | Similarly, we obtain
R_{HQW/GV} order and R_{1/G} order, whereR_{HQW/GV}(\xi )=\frac{\frac{1}{3}\sum _{a=H, Q, W}f(a,\xi )}{\frac{1}{2}\sum _{a=G,
V}f(a,\xi )},andR_{1/G}(\xi )=\frac{1}{f(G,\xi )}.R_{10/10}
order, R_{HQW/GV} order and R_{1/G} order are some cases of
Late-early Ratio Orders.If we choose orders of specie... | {
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} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
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bbf09fa7d654ef9991ea52796ba6b64115b37959 | subsection | 4 | 28 | General variation trends of amino acid frequencies | When sorting the species properly, we can obtain a set of variation
trends for the 20 amino acids. The variation trends are generally
common for different proper orders of species, and the results of
variation trends are also common either based on the data of species
in PEP or based on the data of species in NCBI. So ... | {
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57ac5ce4013df461b0b3d3b537273f33aaf60331 | subsection | 5 | 28 | Fine structures of the variation of amino acid frequencies | Furthermore, we can observe fine structures and superfine structures
of the variation of amino acid frequencies because f(a(i),\xi ) do
not vary with \xi linearly in general. We choose R_{10/10} order
in studying the variation of amino acid frequencies, which is an
intrinsic order related to the molecular evolution. Ro... | {
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"raw": "Savitzky, A. and Golay, M. J. E. Smoothing and differentiation of data. Anal. Chem. 36, 1627-1639 (1964).",
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06fa70210b55581bbfd7a11d42cc506a7cc29f32 | subsection | 6 | 28 | Fine structures of the variation of amino acid frequencies | As a result, we can observe more steep
variation trends in the sections with small and big series numbers
in the fine structures.In the simulation in Fig. S4, we choose a linear relationship
between parameter t and series number of species N_s, i.e.,
t=t_1(N_s), without consideration of the variation of sample
density.... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
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931de41bab614b7fd029ad7f55084ea23f255997 | subsection | 7 | 28 | Superfine structures of the variation of amino acid frequencies | We prescribe the superfine structures as the fluctuations in the
profiles of the variations of amino acid frequencies. The smoothed
lines corresponding to superfine structures can be obtained by
certain smaller spans according to Savitzky-Golay method (red lines
in Fig. 2). We also sorted the species by R_{10/10} order... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
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0d91fd09837e8574de24bde247a3d544b0f58498 | subsection | 8 | 28 | Variation trends of amino acid frequencies for three domains | It is significant to compare the variation trends of amino acid
frequencies for three domains (eubacteria, archaebacteria, and
eukaryotes). The evolution trends of each of the 20 amino acid
frequencies are the same without exception for three domains (Fig.
4). But there are differences of the ranges of amino acid
frequ... | {
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... | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.01852509006857872,
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... |
7011a0e0d1020807371fb111ca040d51e029037c | subsection | 9 | 28 | Experimental observations | It is well known that base compositions in genomes vary greatly,
which are often referred as GC pressure or GA pressure in molecular
evolution. There are delicate structures in the variation of genomic
base compositions of contemporary species, which are discussed in
details in Ref. .The precise correlations between ge... | {
"cite_spans": [
{
"arxiv_id": "",
"doi": "",
"end": 285,
"openalex_id": "",
"raw": "Forsdyke, D. R., Evolutionary Bioinformatics (Springer, New York, 2006).",
"source_ref_id": "8618976676b509d4f1b1a5762736688ce1276912",
"start": 144
},
{
"arxiv_id": "",
... | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.0030514835380017757,
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... |
0456fd7a4cbc4711adb67945b7090733d81f9d1e | subsection | 10 | 28 | Theoretical Results | The mechanism of the evolution of genomic base compositions can also
be explained by the same model based on genetic code multiplicity
and codon chronology. The simulations of correlations of genomic
base compositions and codon position base compositions (Fig. 6e-6h)
agree with the experimental observations respectivel... | {
"cite_spans": [
{
"arxiv_id": "",
"doi": "",
"end": 783,
"openalex_id": "",
"raw": "Muto A., and Osawa S. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. USA 84, 166-169 (1987).",
"source_ref_id": "bb33a1231206ce0c1aebc4c4b5521e... | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.020009668543934822,
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10ecdcf09235cbd0f55c2ad95fa1420caa951154 | subsection | 11 | 28 | Relationships between amino acid frequencies and
genomic base compositions | There is explicit relationship between amino acid frequencies and
genomic base compositions. We observe that the genomic GC content
decreases linearly with the ratio R_{10/10} (Fig. 7a) . Similar results are also valid for other
Late-early Ratio Orders. So the genomic GC content and the amino
acid frequencies are not i... | {
"cite_spans": [
{
"arxiv_id": "",
"doi": "",
"end": 187,
"openalex_id": "",
"raw": "Sueoka N. Correlation between base composition of deoxyribonucleic acid and amino acid composition of protein. Proc. Natl. Acad. Sci. USA 47, 1141-1149 (1961).",
"source_ref_id": "b2bd4efc5d19... | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.03491559997200966,
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... |
f8e4a8f07f061e3a313ba4b59a2ccf8aca84cdfd | subsection | 12 | 28 | Relationships between amino acid frequencies and average protein lengths | There is also correlation between the average protein length
\bar{l} and the ratio R_{HQW/GV} (Fig. 8). The distribution of
all species forms a bowed line in the \bar{l} - R_{HQW/GV} plane,
and the closely related species cluster together in the \bar{l} -
R_{HQW/GV} plane (Fig. 8). Roughly speaking, the average protein... | {
"cite_spans": [
{
"arxiv_id": "",
"doi": "",
"end": 1780,
"openalex_id": "",
"raw": "Hornos, J. E. M., and Hornos, Y. M. M., Algebraic Model for the Evolution of the Genetic Code. Phy. Rev. Lett. 71, 4401-4404 (1993).",
"source_ref_id": "418d11dbc9b5f02ded8f987b3221ae1f287ee7... | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
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... |
7f9da77682367ad11b90e0f571273a9a1cc01bb0 | subsection | 13 | 28 | Relationships between amino acid frequencies
and genomic base compositions | According to the simulation, we found that the genetic code
multiplicity can influence both amino acid frequencies and genomic
GC content. So the evolutionary pressure in the overall molecular
evolution originated in the genetic code evolution. The evolutionary
pressure influences the amino acid frequencies, genomic ba... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.034921444952487946,
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283e142314a2df3e42ad52118fd756745d27ddb6 | subsection | 14 | 28 | Timing the mechanism of the variation of amino acid frequencies | The estimation of the time when the variation of amino acid
frequencies appeared firstly will help us seek the mechanism that
determines the variation of amino acid frequencies of contemporary
species. We can explain that the variation of amino acid frequencies
formed before the stage when three domains began to branch... | {
"cite_spans": [
{
"arxiv_id": "",
"doi": "",
"end": 562,
"openalex_id": "",
"raw": "Jordan, I. K. et al. A univeral trend of amino acid gain and loss in protein evolution. Nature 433, 633-638, (2005).",
"source_ref_id": "4cf8a18240857dc1419351307d9209f5edcab9e8",
"start... | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.03235143423080444,
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2a91831245f5a0de1631dd6309dccd35951eaa2c | subsection | 15 | 28 | Initial driving force for molecular evolution | The variations of amino acid frequencies and genomic base
compositions can be explained in a unified theoretical framework
based on genetic code evolution. All the theoretical results in
section 2-4 are based on one model, whose core is the genetic code
multiplicity and chronology. The simulations by the model agree wi... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
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... |
0707d8423193d233d3448650096898229300aa6f | subsection | 16 | 28 | Cracking the genetic code evolution | If our conjecture is reasonable, we found a new method to crack the
genetic code evolution in primordial time by studying the variation
of amino acid frequencies and genomic base compositions of
contemporary species. Especially, there are some detailed
disagreements between theoretical results and experimental
observat... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.01903354935348034,
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0.... |
cff524f55f192a5f0612f8754d9355d14ebd321e | subsection | 17 | 28 | Outline of the model | We proposed a model based on the evolution of genetic code to
explain the variations of amino acid frequencies and base
compositions in species. The model mainly consists of three parts:
(i) generating void protein sequences by formal language; (ii)
generating protein sequences based on genetic code multiplicity; and
(... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.044471628963947296,
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0... |
e9376b0e6f51de043775b714e2926297e1f0f96c | subsection | 18 | 28 | Generation of void protein sequences by formal language | There are two steps in generation of protein sequences in the model:
(1) generating void protein sequences according to tree adjoining
grammars in Fig. S12 ; (2) the leaf \pi in the tree
adjoining grammar will be substituted by amino acids based on the
genetic code multiplicity in Ref. (Fig. S13
and Tab. 3), where the ... | {
"cite_spans": [
{
"arxiv_id": "",
"doi": "",
"end": 307,
"openalex_id": "",
"raw": "Joshi, A. K. and Schabes, Y., in Handbook of Formal Lan- guages, eds G. Rozenberg and A. Salomma, pp.69-214 (Springer, Heidelberg, 1997).",
"source_ref_id": "ae7e97221e46af7c8fba302e8adcbc4397... | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
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0... |
7600aadfae11a81aac22546927f9ddd2e5e000c4 | subsection | 19 | 28 | Fill in the protein sequences based on genetic code multiplicity | In the second step, the void character \pi in the void protein
sequences will be substituted by 20 amino acids by calling a
subprogram. The rules of substitutions in the subprogram are based
rigorously on the genetic code multiplicity (Fig. S13, Tab. 3).
Namely, \pi may be substituted by either of \pi _1, \pi _2,
\pi _... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
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0... |
78e01ce7cf316c823ca2d6d4067b5ec3e18ba274 | subsection | 20 | 28 | Calculation of amino acid frequencies and their variation trends | When the parameter t is fixed, we can generate sufficient numerous
protein sequences so that the amino acid frequency for each of the
20 amino acids goes to a certain constant value. Then, the amino
acid frequencies vary with parameter t.We can study the evolution of amino acid frequencies by adjusting
the parameter t ... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
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805c563592b2079777a36f937d3080a51f0b11d4 | subsection | 21 | 28 | The mechanism of the variation of amino acid
frequencies in the simulation | According to the simulation by the model, the genetic code
multiplicity plays central role in the evolution of amino acid
frequencies. It should take more steps of substitutions to replace
\pi in the void protein sequences by a late recruited amino acid.
The placements of amino acids in the genetic code multiplicity tr... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.06598605960607529,
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-... |
a37b10850674138275b71caa1e10162797e31905 | subsection | 22 | 28 | Codon chronology | The codon chronology can be reconstructed based on the amino acid
chronology and the primacy of thermostability and complementarity
(Tab. 4) .
The result of codon chronology in Tab. 4 is almost the same as the
chronology in Ref. , but amino acid
chronology in the first line of Tab. 4 in our calculation is
replaced by a... | {
"cite_spans": [
{
"arxiv_id": "",
"doi": "",
"end": 142,
"openalex_id": "",
"raw": "Trifonov, E. N. The triplet code from first principle. J. Biomol. Struct. Dyn. 22, 1-11 (2004)",
"source_ref_id": "b8457a2be4a86761d32d81769730b6241677a382",
"start": 138
},
{
... | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
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... |
c8d8acb46c6e3404812b2b6d3c85ede6267ef527 | subsection | 23 | 28 | Generation of DNA sequences according to codon chronology | There is a one to one relationship between amino acids and a codon
at each of the 32 stages according to the codon chronology in Tab.
5. We separated the section [t_{min}, t_{max}] equally into 32
subsections so that each value of parameter t is in one of these
subsections. Thus, the amino acids in the protein sequence... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.02320202626287937,
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0.... |
fffac3329eb1c4071a48bde8aa8b7ec722da6ea1 | subsection | 24 | 28 | Calculation of genomic base compositions and their variation trends | For a fixed value of parameter t, which corresponds to a certain
stage, we can obtain numerous DNA sequences. Then we can calculate
the compositions of bases G, C, A, T. At last, we can obtain GC
content or GA content at certain codon positions and the total GC
content or GA content in all the DNA sequences. When the p... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
0.0033021392300724983,
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0.... |
532ea3ad14f0c6196e13653001b13f24f0eb9a34 | subsection | 25 | 28 | The mechanism of the variation of genomic base
compositions in the simulation | According to the simulation in the model, the variation of base
compositions in contemporary species can be explained by the codon
chronology, genetic code multiplicity and amino acid chronology
together. For instance, we can explain the relationship between
genomic GC content and GC content at the first, second and th... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
-0.021622182801365852,
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0.... |
c25c99a9ed7425509fb6f7327287e1757bfb02f8 | subsection | 26 | 28 | Relationships between amino acid frequencies and
average protein lengths | When the parameter t is fixed, a group of proteins can be
generated by the model. So both the amino acid frequencies and
average protein length can be calculated together. When t varies,
we can obtain the relationship between R_{HQW/GV} and average
protein length \bar{l} (Fig. 8, Embedded), which agrees with the
experi... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
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dda1431c7aaa753aaf83b4871e41e629f9a9a500 | subsection | 27 | 28 | Conclusion | The variation of amino acid frequencies and the variation of genomic
base compositions can be explained in a unified framework based on
genetic code evolution. According to the model, we show that the
genetic code multiplicity plays central roles in explanation of the
variation of amino acid frequencies of contemporary... | {
"cite_spans": []
} | 10.1016/j.physa.2009.06.017 | 0807.1762 | Genetic code evolution as an initial driving force for molecular
evolution | [
"Dirson Jian Li",
"Shengli Zhang"
] | [
"q-bio.GN"
] | 2,008 | en | Quantitative Biology | [
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189676db9a6450068cd4fc5097960443e9f3844f | abstract | 0 | 8 | Abstract | We report high spatial resolution 11.2 and 18.1 micron imaging of V838
Monocerotis obtained with Gemini Observatory's Michelle instrument in 2007
March. Strong emission is observed from the unresolved stellar core of V838 Mon
in our Gemini imagery, and is confirmed by Spitzer MIPS 24 micron imaging
obtained in 2007 Apr... | {
"cite_spans": []
} | 10.1086/591735 | 0807.1763 | High Spatial Resolution Mid-IR Imaging of V838 Monocerotis: Evidence of
New Circumstellar Dust Creation | [
"John P. Wisniewski",
"Mark Clampin",
"Karen S. Bjorkman",
"Richard K. Barry"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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e6390bc1adce176594c543e48c4e73792e87a78a | subsection | 1 | 8 | Introduction | V838 Monocerotis experienced three photometric outbursts in
early 2002, beginning with an initial event on 2002 January 6.6 and continuing with
events in 2002 February and 2002 March , . The
star's spectrum cooled through the F, G, and K spectral types throughout
February , transitioned to a late M-type giant by 2002 A... | {
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... | 10.1086/591735 | 0807.1763 | High Spatial Resolution Mid-IR Imaging of V838 Monocerotis: Evidence of
New Circumstellar Dust Creation | [
"John P. Wisniewski",
"Mark Clampin",
"Karen S. Bjorkman",
"Richard K. Barry"
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3d2b14537e056d46b34fdfb1b07b137148d8e536 | subsection | 2 | 8 | Observations | We obtained N^{^{\prime }} (11.2\mu m) and Q_{a} (18.1\mu m) imaging of V838 Mon on
2007 March 21-22 using Gemini Obervatory's Michelle imager. Michelle is a 320 x 240 pixel array
which has a 320 x 240 field of view (01 per pixel).
All observations were obtained using a standard chop-nod mode with the same instrument c... | {
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... | 10.1086/591735 | 0807.1763 | High Spatial Resolution Mid-IR Imaging of V838 Monocerotis: Evidence of
New Circumstellar Dust Creation | [
"John P. Wisniewski",
"Mark Clampin",
"Karen S. Bjorkman",
"Richard K. Barry"
] | [
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7ee8163bce7d3ae2117eb0627a8648fe750f0034 | subsection | 3 | 8 | Photometry of the Unresolved Point Source | We used simple aperture photometry to extract flux densities for the unresolved V838 Mon point source in our
Gemini data. We explored the use of 5 circular apertures having radii ranging in size from 06-30 for our
N^{^{\prime }} data and from 07-30 for our Q_{a} data, and found consistent results from each.
The mean fl... | {
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New Circumstellar Dust Creation | [
"John P. Wisniewski",
"Mark Clampin",
"Karen S. Bjorkman",
"Richard K. Barry"
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23df5f66434eb6be93e054e58d11fa5c136cfcc1 | subsection | 4 | 8 | Extended Emission | Gemini's Michelle provides a 10-fold improvement in spatial resolution compared to Spitzer's MIPS; hence, our data
provide us the unique opportunity to search for mid-IR extended emission interior to that probed by .
Comparison of median azimuthally averaged radial profiles of our 11.2\mu m and 18.1\mu m imagery of
V83... | {
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New Circumstellar Dust Creation | [
"John P. Wisniewski",
"Mark Clampin",
"Karen S. Bjorkman",
"Richard K. Barry"
] | [
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06003233fed326e2a3063616c98c10d1e653f9f8 | subsection | 5 | 8 | Extended Emission | This is exactly the flux density one would
expect to see if the extended emission component did not vary between 2004 and 2007,
given the reported 2004 extended emission flux of 0.91 Jy and our use of a scaling factor of 1.97, i.e.24\mu m_{2007} - (1.97 \times 24\mu m_{2004}) = 24\mu m_{net}0.91 Jy - (1.97 \times 0.91 ... | {
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} | 10.1086/591735 | 0807.1763 | High Spatial Resolution Mid-IR Imaging of V838 Monocerotis: Evidence of
New Circumstellar Dust Creation | [
"John P. Wisniewski",
"Mark Clampin",
"Karen S. Bjorkman",
"Richard K. Barry"
] | [
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99f73af83b212d0526fe96ab2a204566a773b235 | subsection | 6 | 8 | Discussion | We detect no
evidence of extended 18.1 \mu m emission above a level of \sim 7 mJy from radial distances of
1860 AU (03) to 93000 AU (150), assuming a distance of 6.2 kpc . Making
the simple assumption that V838 Mon's circumstellar ejecta expands at a constant velocity, this gap of thermal IR
emission suggests no circum... | {
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"ope... | 10.1086/591735 | 0807.1763 | High Spatial Resolution Mid-IR Imaging of V838 Monocerotis: Evidence of
New Circumstellar Dust Creation | [
"John P. Wisniewski",
"Mark Clampin",
"Karen S. Bjorkman",
"Richard K. Barry"
] | [
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70a69cfbbecf53927c9dcd82f8b377c3ddd6a9e0 | subsection | 7 | 8 | Discussion | The enhanced flux at 18.1, 24, and 70 \mu m we observed in 2007
suggests that the equally strong (2007 epoch) 11.2 \mu m
flux might not represent an additional enhancement of gas-phase molecular emission above that suggested by
, but rather represents a warm thermal dust emission component.Early post-outburst polarimet... | {
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... | 10.1086/591735 | 0807.1763 | High Spatial Resolution Mid-IR Imaging of V838 Monocerotis: Evidence of
New Circumstellar Dust Creation | [
"John P. Wisniewski",
"Mark Clampin",
"Karen S. Bjorkman",
"Richard K. Barry"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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47a5ab30d3814d77b50dfa08a2997cd3ed74fe1c | abstract | 0 | 8 | Abstract | We numerically investigate the six-species predator-prey game in complex
networks as well as in $d$-dimensional hypercubic lattices with $d=1,2,..., 6$.
The interaction topology of the six species contains two loops, each of which
is composed of cyclically predating three species. As the mutation rate $P$ is
lowered be... | {
"cite_spans": []
} | 10.1103/PhysRevE.79.066114 | 0807.1764 | Reentrant phase transition in a predator-prey model | [
"Sung-Guk Han",
"Su-Chan Park",
"Beom Jun Kim"
] | [
"cond-mat.stat-mech",
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] | 2,008 | en | Physics | [
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c8c0f489b98154fb44a430e762ad7ee0f07a1c7c | subsection | 1 | 8 | Introduction | Recently, nonequilibrium dynamical systems as well as
standard equilibrium statistical mechanical model systems have been intensively
studied in the interaction
structure of complex networks .
Effects of shortcuts in the Watts-Strogatz (WS) networks
on collective dynamic behaviors have been drawn much attention,
revea... | {
"cite_spans": []
} | 10.1103/PhysRevE.79.066114 | 0807.1764 | Reentrant phase transition in a predator-prey model | [
"Sung-Guk Han",
"Su-Chan Park",
"Beom Jun Kim"
] | [
"cond-mat.stat-mech",
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] | 2,008 | en | Physics | [
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aa80c6676dab6f6b0580555be3e6c2a4d0b4bd86 | subsection | 2 | 8 | Introduction | Specifically, Szabó et al. have shown
that the predator-prey game played on a 2D regular lattice
exhibits a phase transition of the 2D Ising universality as the mutation
rate is changed, and also identified
the relevant order parameter detecting the Z_2 symmetry breaking
of the defensive alliance of three cyclically p... | {
"cite_spans": []
} | 10.1103/PhysRevE.79.066114 | 0807.1764 | Reentrant phase transition in a predator-prey model | [
"Sung-Guk Han",
"Su-Chan Park",
"Beom Jun Kim"
] | [
"cond-mat.stat-mech",
"q-bio.PE"
] | 2,008 | en | Physics | [
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5e52887727fbc5556b04f92703a98cfac20846d2 | subsection | 3 | 8 | Defensive alliance process | We start from the description of how the DAP is implemented on general
networks.
The algorithm for the simulations is as follows:
Initially at time t=0, six species are equally distributed on vertices
of the given network structure, with the density c_s of the species
s given by c_s(t=0) = 1/6 for all species (s=0,1, \... | {
"cite_spans": []
} | 10.1103/PhysRevE.79.066114 | 0807.1764 | Reentrant phase transition in a predator-prey model | [
"Sung-Guk Han",
"Su-Chan Park",
"Beom Jun Kim"
] | [
"cond-mat.stat-mech",
"q-bio.PE"
] | 2,008 | en | Physics | [
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60a7b0b1d995841575c230cf59949b3a104a9b67 | subsection | 4 | 8 | DAP in the WS networks | We first construct WS networks for the DAP as follows :
(i) 1D and 2D regular lattices are first built.
For 1D each vertex has connections to its four neighbors (nearest
and next-nearest neighbors), whereas for 2D we assume only
four nearest neighbor connections. (ii) With the rewiring probability
\alpha one end of eac... | {
"cite_spans": []
} | 10.1103/PhysRevE.79.066114 | 0807.1764 | Reentrant phase transition in a predator-prey model | [
"Sung-Guk Han",
"Su-Chan Park",
"Beom Jun Kim"
] | [
"cond-mat.stat-mech",
"q-bio.PE"
] | 2,008 | en | Physics | [
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0c006ca94b807e2506ec32f4108cac076c525369 | subsection | 5 | 8 | DAP in the WS networks | At \alpha = 0,WS_1 and WS_2 correspond to the regular 1D and 2D lattices.(c) m versus \alpha for the WS_2 networks of the sizesN=256 \times 256 and 512 \times 512 with \mu set to 6.0, followingthe vertical arrow in (b). The reentrant behavior is again seen veryclearly.]It is very interesting that the phase diagrams in ... | {
"cite_spans": []
} | 10.1103/PhysRevE.79.066114 | 0807.1764 | Reentrant phase transition in a predator-prey model | [
"Sung-Guk Han",
"Su-Chan Park",
"Beom Jun Kim"
] | [
"cond-mat.stat-mech",
"q-bio.PE"
] | 2,008 | en | Physics | [
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dbce65737a17fd23fb900ff5d52c753ef1c0dbe7 | subsection | 6 | 8 | DAP in the WS networks | It appears that \alpha ^*
is close to the value of \alpha at the end point of the lob
structure in the phase diagram, i.e., \alpha ^* \approx 0.1 for the
WS_1 network.
[Figure: (Color online) Phase transitions in 3D [for (a)-(c)], 4D [for (d)-(f)],and 5D [for (g)-(i)] regular hypercubic lattices in terms of the mutatio... | {
"cite_spans": []
} | 10.1103/PhysRevE.79.066114 | 0807.1764 | Reentrant phase transition in a predator-prey model | [
"Sung-Guk Han",
"Su-Chan Park",
"Beom Jun Kim"
] | [
"cond-mat.stat-mech",
"q-bio.PE"
] | 2,008 | en | Physics | [
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db1eaf13d4c3741c00ff9fb6b9daa31da1341aa4 | subsection | 7 | 8 | DAP in 3-, 4-, and 5-dimensional regular lattices | The results in three-, four-, and five-dimensional regular hypercubic lattices
are given in Fig. REF
for hypercubic lattices with the linear size L (the total number of individual species N = L^d).
We use the system size L=16, 20, 24, 28, 32, and 48 for 3D,
L=12, 14, 16, 18, and 20 for 4D, and L=8, 10, 12 and 14 for 5... | {
"cite_spans": []
} | 10.1103/PhysRevE.79.066114 | 0807.1764 | Reentrant phase transition in a predator-prey model | [
"Sung-Guk Han",
"Su-Chan Park",
"Beom Jun Kim"
] | [
"cond-mat.stat-mech",
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] | 2,008 | en | Physics | [
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48c3de3af53f9ceca280794a12d12c890bb784be | abstract | 0 | 19 | Abstract | We present the first multi-color view of the scattered light disk of the
Herbig Ae star HD 163296, based on coronagraphic observations from the Hubble
Space Telescope Advanced Camera for Surveys (ACS). Radial profile fits of the
surface brightness along the disk's semi-major axis indicates that the disk is
not continuo... | {
"cite_spans": []
} | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
";"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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c2b34087e78c7c75c6c0be68c955123b10545fc9 | subsection | 1 | 19 | Introduction | Investigations of the nature and evolution of dust grains in proto-planetary systems are
motivated in part by our desire to understand the birth and evolution of planetary bodies,
which originate from these systems. It is well established that Herbig
Ae/Be stars are
intermediate mass pre-main-sequence stars, analogous ... | {
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"ope... | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
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4a7d576f5b84773708f46a0b7aa74c8371c97f3e | subsection | 2 | 19 | Introduction | The possible mechanisms
which might explain the observed scattered light variability are discussed in
Section . We provide a summary of our main results in Section . | {
"cite_spans": []
} | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
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69020ac9c2589f745404efa639c45bc25798672b | subsection | 3 | 19 | Observations and Data Reduction | We obtained coronagraphic imaging of HD 163296 in the HST ACS F435W filter via the
cycle 12 GTO program 9987, and in the ACS F606W and F814W filters via the cycle 11
GTO program 9295. All observations utilized
the coronagraphic mode of the High Resolution
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"John P. Wisniewski",
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"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
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877f563799484abd87f7e5f2c57cef837642e26f | subsection | 4 | 19 | Disk Characteristics Derived from HST ACS Observations | Figures REF , REF , and REF present the PSF-subtracted, roll angle
combined, calibrated images of HD 163296 in the F435W, F606W,
and F814W filters respectively, using a square-root intensity stretch and a 3 pixel
Gaussian kernel smoothing function. We have masked regions interior to a radial distance
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... | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
";"
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5b1745883ee32d7afd1d9dd272938fed7f8c2b9d | subsection | 5 | 19 | Disk Surface Brightness | While the surface brightness profile of portions of the HD 163296 disk were characterized
via white-light STIS coronagraphic imaging , the large occulting wedges used
by this coronagraph prevents an investigation of the full radial and azimuthal structure
of the disk. Our ACS images do not suffer from such artifacts, h... | {
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"source_ref_id": "045fbd992b5015c857d8... | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
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ea3f70aaa2be20521c7387079f5d9c2cf199d6b8 | subsection | 6 | 19 | Disk Surface Brightness | As the 1998
epoch STIS data are significantly fainter than that measured in each bandpass of our ACS data,
it is clear that no combination of the ACS data can reproduce the behavior of the
STIS scattered light surface brightnesses. We suggest that the observed multi-epoch behavior
of the disk's surface brightness is on... | {
"cite_spans": []
} | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
";"
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"astro-ph"
] | 2,008 | en | Physics | [
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6ebd6216e142c092ceaa12acfac42d3dbc3cb4bb | subsection | 7 | 19 | Disk Size | A large range of sizes have been suggested for the HD 163296 circumstellar disk.
assumed an outer radius of 50 AU in their SED fitting of the system. reported that CO
emission, likely produced in the upper layers of the disk, extended out to a radial distance of 540 AU;
moreover, they reported an unexpected deficit of... | {
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Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
";"
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c6ffd8f97b5892a01df5edc28b9597123d799a6e | subsection | 8 | 19 | Disk Geometry | Power-law fits to scattered light imagery provide one means to diagnose the geometry of Herbig
Ae circumstellar disks (see e.g. ). As seen in Table REF , the surface
brightness of the HD 163296 disk in the ACS F435W, F606W, and F814W filters follow a
\sim r^{-4} dependence. These data clearly deviate from the expected ... | {
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... | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
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"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
";"
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ceef16de958ea58f5b1af7cd8276627ab76d632d | subsection | 9 | 19 | Disk Color | Our multi-filter HST ACS dataset also allows us to provide the first measurement of
the color of HD 163296's scattered light disk. We first calculated the surface
brightness at radial distances of 30 and 35 along the disk semi-major
axis (PAs of 132^{\circ } and 312^{\circ }). The median flux within 10 x 10
apertures w... | {
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"end": 1... | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
";"
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3a7238d5c6aaa22f234019b18571209519e2a57e | subsection | 10 | 19 | Disk Color | The detection of a non-continuously flared disk and red (V-I) disk color
from our spatially resolved scattered light imagery is thus consistent (though not conclusive)
with such phenomenon occurring. We also note that our HD 163296 imagery does not exhibit
significant evidence of a scattering asymmetry due to differenc... | {
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"John P. Wisniewski",
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"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
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5c456889410e0ec34f9b8fbca10483c10b519e15 | subsection | 11 | 19 | Morphological Features | The superlative spatial resolution of the HST ACS allows for the search of both radial
and azimuthal morphological structures within the HD 163296 scattered light disk.
Simple visual inspection of our F606W and F814W images
(Figure REF )
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"source_ref_id": "045fbd992b5015c857d8... | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
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9957acd9229fbf1cf299182fd71f60d3d5af1a0b | subsection | 12 | 19 | Morphological Features | Note that our ACS radial profile cuts correspond to the median average of a
10 pixel wide (025 arcsec) aperture which were subsequently averaged in 3
(radial) pixel bins, while our STIS radial profile cuts correspond to the median average
of a 5 pixel wide (025 arcsec) aperture which were subsequently averaged in
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"source_ref_id": "045fbd992b5015c857d8... | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
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c3fb7c63960d337a7d74c1ed655bb6496cd314e0 | subsection | 13 | 19 | The Multi-Epoch Behavior of the HD 163296 Scattered Light Disk | presented white-light HST STIS coronagraphic observations of HD 163296,
obtained in September 1998. The STIS observations were characterized by a featureless signal
from 15 to 25, a darker zone at 265 of width 04, and two bright
ansae peaking at 29 in the SE quadrant and 32 in the NW quadrant (see
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consid... | {
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"source_ref_id": "045fbd992b5015c857d8... | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
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"David R. Ardila",
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"David A. Golimowski",
"Garth D. Illingworth",
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e6ba45805324b0650d348384ac396d781563b6bb | subsection | 14 | 19 | Origin of the Observed Scattered Light Variability | Our analysis of multi-epoch, multi-color spatially resolved imagery of HD 163296
suggests that its scattered light disk is variable; we observe a \sim 1 mag arcsec^{-2}
change in the overall surface brightness of the disk between epochs of observations, variability in the
visibility of ansa structure(s),
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3cd46a2686a2fe54ea75b32a1c11f2fd121503bd | subsection | 15 | 19 | Origin of the Observed Scattered Light Variability | One suggested
method to produce a self-shadowed disk is by inflation of the inner
disk wall, which prevents copious amounts of photons from reaching at least
part of the outer (flatter) disk. has noted that the infrared spectral energy
distribution (IR SED) of HD 163296 can vary by \sim 30% on time-scales of 3 years
or... | {
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... | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
";"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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30fe8073966708347dd690a780964aa13452b389 | subsection | 16 | 19 | Origin of the Observed Scattered Light Variability | We speculate that
the inner disk wall might be azimuthally asymmetric, hence cast an azimuthally
asymmetric shadow on the outer disk. Given the
orbital period of material located at the inner wall sublimation radius, \le 1 week
(Sitko 2007, personal communication), the time-scale for such a asymmetry to produce
a brigh... | {
"cite_spans": []
} | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
";"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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18bc42ae89cc5c7b3457131da4241a4313e9f3eb | subsection | 17 | 19 | Summary | We have presented the first multi-color, multi-epoch analysis of resolved optical
scattered light imaging of the Herbig Ae star HD 163296. To summarize the
observational properties of these data:We spatially resolved the HD 163296 scattered light disk over radial
distances of 29-44 (350-540 AU) in the HST/ACS F435W, F6... | {
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"source_ref_id": "045fbd992b5015c857d... | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
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bd00052a3123b296910dd04484c8012a4c084c2f | subsection | 18 | 19 | Summary | Based on the short (\le 1 week, Sitko 2007 personal communication) orbital
time-scale of material located at the inner wall, we suggest that a series of resolved
scattered light images of HD 163296, obtained during an epoch of enhanced self-shadowing,
would provide a test of this particular suggested phenomenon.We than... | {
"cite_spans": []
} | 10.1086/589629 | 0807.1766 | The HD 163296 Circumstellar Disk in Scattered Light: Evidence of
Time-Variable Self-Shadowing | [
"John P. Wisniewski",
"Mark Clampin",
"Carol A. Grady",
"David R. Ardila",
"Holland C. Ford",
"David A. Golimowski",
"Garth D. Illingworth",
"John E. Krist",
";"
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aca4b1992a0448546c752ec36d3b64867df36228 | abstract | 0 | 13 | Abstract | We report the discovery of an exact mapping from Galilean time and space
coordinates to Minkowski spacetime coordinates, showing that Lorentz covariance
and the spacetime construct are consistent with the existence of a dynamical
3-space, and "absolute motion". We illustrate this mapping first with the
standard theory ... | {
"cite_spans": []
} | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
"Reginald T Cahill"
] | [
"physics.gen-ph"
] | 2,008 | en | Physics | [
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b30640503c2e2229ed4bdeae080a128c350edd56 | subsection | 1 | 13 | Introduction | It is commonly argued that the manifest success of Lorentz covariance and the spacetime formalism in Special Relativity (SR) is inconsistent with the anisotropy of the speed of light, and indeed the existence of absolute motion, that is, a detectable motion relative to an actual dynamical 3-space, despite the repeated ... | {
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"raw": "Minkowski H. “Raum und Zeit”, Physikalische Zeitschrift, 10 Jahrgang, 104-115, 1909. English translation in The Principle of Relativity by Lorentz H.A., Einstein A., Minkowski H. and Weyl H., transl... | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
"Reginald T Cahill"
] | [
"physics.gen-ph"
] | 2,008 | en | Physics | [
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644f2f2119ad2ad8d09f2b29b78918beefd2112b | subsection | 2 | 13 | Introduction | The conclusion is that Lorentz covariance and the spacetime formalism are artifacts of the use of peculiar non-physical space and time coordinates. The use of this class of coordinates has confounded 20th century physics, and lead to the existence of a “flowing" dynamical 3-space being overlooked. The dynamics of this ... | {
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"en... | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
"Reginald T Cahill"
] | [
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] | 2,008 | en | Physics | [
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8942e0a135018338adaac85822ccad52a62c8d8a | subsection | 3 | 13 | Introduction | These cavity experiments are based on two mistaken notions: (i) that a breakdown of Lorentz symmetry is related to the existence of a preferred frame, and (ii) that vacuum-mode Michelson interferometers can detect a light speed anisotropy associated with such a preferred frame..There are now four different experimental... | {
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"end"... | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
"Reginald T Cahill"
] | [
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] | 2,008 | en | Physics | [
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780dad1c054054968f13cc33088999bc1db30078 | subsection | 4 | 13 | Sound Wave Galilean Covariant Formalism | Let us first use the example of sound waves to discuss the mapping from Galilean space and time coordinates to Minkowski-Einstein spacetime coordinates - as in this case the underlying physics is well understood.
The standard formulation for sound waves in a moving fluid is\left(\frac{\partial }{\partial t} +{\bf v}({\... | {
"cite_spans": []
} | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
"Reginald T Cahill"
] | [
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91ee1dd843054c7afffbb7bf6dc1ba5ae43dcc0c | subsection | 5 | 13 | Sound Wave Galilean Covariant Formalism | Then the physical time and space coordinates of each are related by the Galilean transformationt^\prime &=&t, \\
x^\prime &=&x-Vt, \mbox{\ \ \ }y^\prime =y, \mbox{\ \ \ }z^\prime =z.We have taken the simplest case where V is the relative speed of the two observers in their common x directions. Then the derivatives are ... | {
"cite_spans": []
} | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
"Reginald T Cahill"
] | [
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305c05ec2409616f227a72e67df339f7a1be885d | subsection | 6 | 13 | Sound Wave Lorentz Covariant Formalism | The above Galilean formalism for sound waves is well known and uses physically sensible choices for the time and space coordinates. Of course we could choose to use spherical or cylindrical space coordinates if we so desired. This would cause no confusion. However we could also choose to use a new class of time and spa... | {
"cite_spans": []
} | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
"Reginald T Cahill"
] | [
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23263fac5359519743de1054b3f522a924dc7409 | subsection | 7 | 13 | Sound Wave Lorentz Covariant Formalism | Eqn.(REF ) is now covariant under Lorentz transformationsLorentz did not construct the “Lorentz transformation" - and this nomenclature is very misleading as Lorentz held to a different interpretation of the so-called relativistic effects.,T^\prime &=&\gamma (V)\left(T+\frac{VX}{c^2}\right), \\
X^\prime &=&\gamma (V)(X... | {
"cite_spans": []
} | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
"Reginald T Cahill"
] | [
"physics.gen-ph"
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f55393ba94b2a729a69add44c075b5f635277df2 | subsection | 8 | 13 | Dynamical 3-Space Theory | Here we briefly review the dynamics of the 3-space that is the analogue of the “flowing fluid" in the sound allegory. For zero vorticity we have , , \nabla .\left(\frac{\partial {\bf v} }{\partial t}+ ({\bf v}.{\bf \nabla }){\bf v}\right)+
\frac{\alpha }{8}\left((tr D)^2 -tr(D^2)\right)=-4\pi G\rho ,\nabla \times {\bf ... | {
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"start... | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
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] | [
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bec149099e39b20e8a8b7cb9770adbece75a5e3c | subsection | 9 | 13 | Dynamical 3-Space Theory | Together (REF ) and (REF ) amount to the derivation of gravity as a quantum effect, explaining both the equivalence principle (\bf g in (REF ) is independent of m) and the Lense-Thirring effect. Overall we see, on ignoring vorticity effects, that\nabla .{\bf g}=-4\pi G\rho -\frac{\alpha }{8}\left((tr D)^2 -tr(D^2)\righ... | {
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"raw": "Cahill R.T. A Quantum Cosmology: No Dark Matter, Dark Energy nor Accelerating Universe, arXiv:0709.2909, 2007.",
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] | [
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391e7c5c87c83454947db7ae30d99c9221670044 | subsection | 10 | 13 | Galilean Covariant Electromagnetic Theory | Hertz in 1890 noted that Maxwell had overlooked the velocity field that accompanies time derivatives, as in (REF ),
and presented an improved formalism, and the minimal source-free form is\mu \left(\frac{\partial }{\partial t}+{\bf v.\nabla }\right) {\bf H}&=&-\nabla \times {\bf E},\\
\epsilon \left(\frac{\partial }{\p... | {
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... | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
"Reginald T Cahill"
] | [
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ebbed3941f000838935c683d366352580dde1c8f | subsection | 11 | 13 | Galilean Covariant Electromagnetic Theory | Transforming to the Minkowski-Einstein T,X,Y,Z coordinates using (REF ) and (REF ) we obtain the form of the source-free “standard" Maxwell equations\frac{\partial ^2 {\bf E}}{\partial T^2} =c^2\overline{\nabla }^2{\bf E},\mbox{\ \ \ }\frac{\partial ^2 {\bf H}}{\partial T^2} =c^2\overline{\nabla }^2{\bf H}which is agai... | {
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"raw": "Braxmaier C. et al. Phys. Rev. Lett., 88, 010401, 2002; Müller H. et al. Phys. Rev. D, 68, 116006-1-17, 2003; Müller H. et al. Phys. Rev. D67, 056006,2003; Wolf P. et al. Phys. Rev. D, 70, 051902-1... | 0807.1767 | Unravelling Lorentz Covariance and the Spacetime Formalism | [
"Reginald T Cahill"
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fd744c193415338ccefd284d2bfb9022a63cee8b | subsection | 12 | 13 | Conclusions | We have reported herein the discovery of an exact and invertible mapping from Galilean time and space coordinates to Minkowski-Einstein spacetime coordinates. This mapping removes the effects of the velocity of the dynamical 3-space relative to an observer, and so in this sense the Minkowski-Einstein coordinates are de... | {
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fa7e1fdc21c5651f5cbf9d54887d3d02de76c82a | abstract | 0 | 9 | Abstract | We carefully examine the negative refractive index slab perfect lens theory
by Pendry and point out an inconsistency that can be resolved. As a result, we
find negative index slabs do not amplify or enhance evanescent waves and
therefore they do not make a perfect lens in the sense that was originally
suggested. | {
"cite_spans": []
} | 0807.1768 | Revisiting the Perfect Lens | [
"Weiguo Yang",
"John O. Schenk",
"Michael A. Fiddy"
] | [
"physics.optics"
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7727f968dd13583a588a64b9ee40b1559775a234 | subsection | 1 | 9 | Introduction | In his seminal paper , Pendry derived the fascinating result that a slab of negative index material, despite the fact that evanescent waves would decay away from the interfaces, amplifies the evanescent waves sustaining them through the material to the other side. Since these evanescent waves carry high spatial frequen... | {
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47fb87b1c967927a4e452f1453fce5763a8d1d0c | subsection | 2 | 9 | Pendry’s Negative Index Perfect Lens Formulism | FigureREF shows an interface between two different materials. The (x-z) plane is chosen to be the plane that contains the propagation vector \mathbf {k}=(k_x,k_z) and a normal of the interface. Following Pendry’s notation , when k_x<|\mathbf {k}|, k_z is a real number and plane waves e^{i\mathbf {k}\cdot \mathbf {r}-i\... | {
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ad7eb5048c5480edc183f01c677dc1b971ec6df7 | subsection | 3 | 9 | Pendry’s Negative Index Perfect Lens Formulism | For reflected field, \omega \mu _0(H_{0S-})_x=k_zE_{0S-}, and \omega \mu _0(H_{0S-})_z=k_xE_{0S-}, and for the transmitted field, \omega \mu \mu _0(H_{1S+})_x=-k_zE_{1S+}, and \omega \mu \mu _0(H_{1S+})_z=k_xE_{1S+}. Combining these relations with the boundary conditions, one has equations for the transmitted and refle... | {
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"end... | 0807.1768 | Revisiting the Perfect Lens | [
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9f3d3aa86229fe6e39ba8822c65c70ee263a2282 | subsection | 4 | 9 | A simple solution to the apparent paradox | Consider the situation for which the medium has a negative refractive index for doubly negative materials (\epsilon <0 and \mu <0), and let us assume, for S-polarization, the evanescent wave in this medium takes the form,E_{1S+}=t[0,1,0]\exp (ik^\prime _z z+ik_x x+i\omega t+i\phi )where k^\prime _z is still given by Eq... | {
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"end... | 0807.1768 | Revisiting the Perfect Lens | [
"Weiguo Yang",
"John O. Schenk",
"Michael A. Fiddy"
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"physics.optics"
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a600e8f4786087e9a918dd694eb876b70e7c8850 | subsection | 5 | 9 | A simple solution to the apparent paradox | The z component of the magnetic field is in phase with the y component of the electric field,\omega \mu _0 (H_{0S+})_z=k_x \exp (-|k_z|z)\cos (k_x x-\omega t+\phi _0),which indicates that there will be energy flow in the x direction if k_x is nonzero.Similarly for the reflected wave, we have,E_{0S-}=r[0,1,0]\exp (|k_z|... | {
"cite_spans": []
} | 0807.1768 | Revisiting the Perfect Lens | [
"Weiguo Yang",
"John O. Schenk",
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f8698a4cb0cd96d48bef6a60013fecd08aac8b3d | subsection | 6 | 9 | A simple solution to the apparent paradox | Consequently, Eq.REF become,1+r&=&t \\
-|k_z|+|k_z|r&=&\frac{|k^\prime _z|}{\mu }twhich give the transmission and reflection coefficients for evanescent waves at the interface with the negative index medium,t&=&\frac{2\mu |k_z|}{\mu |k_z|-|k^\prime _z|} \\
r&=&\frac{\mu |k_z|+|k^\prime _z|}{\mu |k_z|-|k^\prime _z|},Thi... | {
"cite_spans": []
} | 0807.1768 | Revisiting the Perfect Lens | [
"Weiguo Yang",
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"Michael A. Fiddy"
] | [
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2ae170214fd5dcea9e8a3e85df50e8a4c9b28be5 | subsection | 7 | 9 | Another equivalent interpretation | Consider equivalent solutions to the Helmholz equation, \exp [-i(\omega t-\mathbf {k}\cdot \mathbf {r})] and \exp [-i(\omega t+\mathbf {k}\cdot \mathbf {r})], the difference between the two is that their phase velocities are in opposite directions. Using these solutions for positive and negative index media respectivel... | {
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"Weiguo Yang",
"John O. Schenk",
"Michael A. Fiddy"
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1e8b1a0fa12b0104c7d3567d03f9659cdadff0f6 | subsection | 8 | 9 | Discussion | As mentioned in the introduction, Ref. is cited as an experimental verification of the amplification or enhancement of the evanescent wave in a negative index slab . The maximum transmission of a sliver slab, which serves as a lossy negative index slab, is plotted against the thickness of the slab in Fig.4 of Ref.. The... | {
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"raw": "Z. Liu, N. Fang, T.-J. Yen, and X. Zhang, Applied Physics Letters 83, 5184 (2003), URL http://link.aip.org/link/?APL/83/5184/1.",
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... | 0807.1768 | Revisiting the Perfect Lens | [
"Weiguo Yang",
"John O. Schenk",
"Michael A. Fiddy"
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"physics.optics"
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a079b8f54c5dc47e6a9f2e6897c2a6b5ade5e910 | abstract | 0 | 9 | Abstract | In helioseismology, there is a well-known offset between observed and
computed oscillation frequencies. This offset is known to arise from improper
modeling of the near-surface layers of the Sun, and a similar effect must occur
for models of other stars. Such an effect impedes progress in asteroseismology,
which involv... | {
"cite_spans": []
} | 10.1086/591667 | 0807.1769 | Correcting stellar oscillation frequencies for near-surface effects | [
"Hans Kjeldsen",
"Timothy R. Bedding",
"Joergen Christensen-Dalsgaard"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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34989c46021f6ca0b077c5d4b59a498045f86688 | subsection | 1 | 9 | Introduction | Both helio- and asteroseismology involve comparing observed oscillation
frequencies with those calculated from theoretical models. However, for
the Sun there is a long-standing systematic offset between observed and
computed frequencies that is known to arise from improper modeling of the
near-surface layers , , , . Th... | {
"cite_spans": [
{
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"raw": "Christensen-Dalsgaard, J., Däppen, W., & Lebreton, Y., 1988, Nat, 336, 634.",
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"start": 131
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{
"arxiv_id": "",... | 10.1086/591667 | 0807.1769 | Correcting stellar oscillation frequencies for near-surface effects | [
"Hans Kjeldsen",
"Timothy R. Bedding",
"Joergen Christensen-Dalsgaard"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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cc051f0c9c58cb0fd9130e0c11305997ff8d6e18 | subsection | 2 | 9 | Method | The p-mode oscillations in solar-type stars for a given angular degree l
are approximately equally spaced in frequency, with a separation of \mbox{$\Delta \nu $}
(the so-called large separation; see for a review of the
theory of solar-like oscillations). Since the offset from incorrect
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... | 10.1086/591667 | 0807.1769 | Correcting stellar oscillation frequencies for near-surface effects | [
"Hans Kjeldsen",
"Timothy R. Bedding",
"Joergen Christensen-Dalsgaard"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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11eafb8d4e1b45e07aca64be8800017906b9d2ae | subsection | 3 | 9 | Method | From homology
scaling it then follows that, to a good approximation,\nu _{\rm best}(n) = r \nu _{\rm ref}(n),where the scaling factor r is related to the mean densities
\bar{\rho }_{\rm best} and \bar{\rho }_{\rm ref} of the best and reference
models by\bar{\rho }_{\rm best} = r^2 \bar{\rho }_{\rm ref}.Given a determin... | {
"cite_spans": []
} | 10.1086/591667 | 0807.1769 | Correcting stellar oscillation frequencies for near-surface effects | [
"Hans Kjeldsen",
"Timothy R. Bedding",
"Joergen Christensen-Dalsgaard"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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ba9035e6149aafaf8824f45b05ec4933c63db837 | subsection | 4 | 9 | Method | For \nu _{\rm obs}(n) and \nu _{\rm ref}(n), we simply use
the means of the given sets of frequencies, which we denote by \langle \nu _{\rm obs}(n) \rangle and \langle \nu _{\rm ref}(n) \rangle .To estimate the large separations, we calculate the slope of a linear
least-squares fit to the given frequencies (as a functi... | {
"cite_spans": []
} | 10.1086/591667 | 0807.1769 | Correcting stellar oscillation frequencies for near-surface effects | [
"Hans Kjeldsen",
"Timothy R. Bedding",
"Joergen Christensen-Dalsgaard"
] | [
"astro-ph"
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57cb48f56b680391bf2fcc47a5ad8b864601d5c9 | subsection | 5 | 9 | Application to the Sun | For the Sun we took Model S of , as listed in the first row
of Table . We assumed this to be the “best” solar model,
in the sense defined above, which means we can set r=1 (see
equation REF ). For the observed solar frequencies, we used
those measured by with the GOLF instrument on the SOHO
spacecraft.We followed the p... | {
"cite_spans": [
{
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"doi": "",
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"start": 0
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"arxiv_id"... | 10.1086/591667 | 0807.1769 | Correcting stellar oscillation frequencies for near-surface effects | [
"Hans Kjeldsen",
"Timothy R. Bedding",
"Joergen Christensen-Dalsgaard"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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027959e900af053aab62e71cdf12fee168341349 | subsection | 6 | 9 | Application to | We have considered three stars for which observations and models have been
published. For \alpha Cen A we took observed frequencies (radial modes only)
from four sources: , , and
. This gave a set of 33 measured frequencies for 11 orders,
all of which were given equal weight in the fitting process. For \alpha Cen B
t... | {
"cite_spans": [
{
"arxiv_id": "",
"doi": "",
"end": 182,
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"raw": "Bouchy, F., & Carrier, F., 2002, A&A, 390, 205.",
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"start": 86
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"end"... | 10.1086/591667 | 0807.1769 | Correcting stellar oscillation frequencies for near-surface effects | [
"Hans Kjeldsen",
"Timothy R. Bedding",
"Joergen Christensen-Dalsgaard"
] | [
"astro-ph"
] | 2,008 | en | Physics | [
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