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Symmetry, Volume 2, Issue 2 (June 2010), Pages 437-1200

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Open AccessArticle Experimental Test of L- and D-Amino Acid Binding to L- and D-Codons Suggests that Homochirality and Codon Directionality Emerged with the Genetic Code
Symmetry 2010, 2(2), 1180-1200; https://doi.org/10.3390/sym2021180
Received: 9 June 2010 / Revised: 18 June 2010 / Accepted: 22 June 2010 / Published: 23 June 2010
Cited by 3 | PDF Full-text (1010 KB)
Abstract
L-amino acids bind preferentially to their D-codons, but almost nothing is known about whether D-amino acids correspondingly prefer L-codons, or how codon directionality affects amino acid binding. To investigate these issues, two D-RNA-oligonucleotides having inverse base sequences (D-CGUA and D-AUGC) and their corresponding
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L-amino acids bind preferentially to their D-codons, but almost nothing is known about whether D-amino acids correspondingly prefer L-codons, or how codon directionality affects amino acid binding. To investigate these issues, two D-RNA-oligonucleotides having inverse base sequences (D-CGUA and D-AUGC) and their corresponding L-RNA-oligonucleotides (L-CGUA and L-AUGC) were synthesized and their affinity determined for Gly and eleven pairs of L- and D-amino acids. The data support the hypothesis (Root-Bernstein, Bioessays 2007; 29: 689–698) that homochirality and codon directionality emerged as a function of the origin of the genetic code itself. Further tests involving amplification methods are proposed. Full article
(This article belongs to the Special Issue Symmetry of Life and Homochirality)
Open AccessReview A Critical Assessment of the Performance of Magnetic and Electronic Indices of Aromaticity
Symmetry 2010, 2(2), 1156-1179; https://doi.org/10.3390/sym2021156
Received: 17 February 2010 / Revised: 7 May 2010 / Accepted: 10 June 2010 / Published: 14 June 2010
Cited by 72 | PDF Full-text (711 KB)
Abstract
The lack of reference aromatic systems in the realm of inorganic aromatic compounds makes the evaluation of aromaticity in all-metal and semimetal clusters a difficult task. To date, calculation of nucleus-independent chemical shifts (NICS) has been the most widely used method to discuss
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The lack of reference aromatic systems in the realm of inorganic aromatic compounds makes the evaluation of aromaticity in all-metal and semimetal clusters a difficult task. To date, calculation of nucleus-independent chemical shifts (NICS) has been the most widely used method to discuss aromaticity in these systems. In the first part of this work, we briefly review our previous studies, showing some pitfalls of the NICS indicator of aromaticity in organic molecules. Then, we refer to our study on the performance of some aromaticity indices in a series of 15 aromaticity tests, which can be used to analyze the advantages and drawbacks of aromaticity descriptors. It is shown that indices based on the study of electron delocalization are the most accurate among those analyzed in the series of proposed tests, while NICS(1)zz and NICS(0)πzz present the best behavior among NICS indices. In the second part, we discuss the use of NICS and electronic multicenter indices (MCI) in inorganic clusters. In particular, we evaluate the aromaticity of two series of all-metal and semimetal clusters with predictable aromaticity trends by means of NICS and MCI. Results show that the expected trends are generally better reproduced by MCI than NICS. It is concluded that NICS(0)π and NICS(0)πzz are the kind of NICS that perform the best among the different NICS indices analyzed for the studied series of inorganic compounds. Full article
(This article belongs to the Special Issue Aromaticity and Molecular Symmetry)
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Open AccessReview A Review of New Analytic Techniques for Quantifying Symmetry in Locomotion
Symmetry 2010, 2(2), 1135-1155; https://doi.org/10.3390/sym2021135
Received: 12 May 2010 / Revised: 9 June 2010 / Accepted: 10 June 2010 / Published: 14 June 2010
Cited by 16 | PDF Full-text (656 KB)
Abstract
We present a review of novel techniques developed by our research group to improve quantitative assessment of human movement, especially assessments related to symmetric and asymmetric gait patterns. These new methods use motion capture data of the lower limb joints (e.g., joint and
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We present a review of novel techniques developed by our research group to improve quantitative assessment of human movement, especially assessments related to symmetric and asymmetric gait patterns. These new methods use motion capture data of the lower limb joints (e.g., joint and body segment angular position and/or velocity, or joint center locations) and include: (1) Regions of Deviation (ROD) analysis, (2) complexity and variability of phase portraits, and (3) multivariate shape-alignment and decomposition. We provide example demonstrations of these techniques using data from infants, typical and atypically developing children, simulated injuries of a knee or ankle, and wheelchair propulsion. Full article
(This article belongs to the Special Issue Complexity and Symmetry)
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Open AccessReview Symmetry in Boolean Satisfiability
Symmetry 2010, 2(2), 1121-1134; https://doi.org/10.3390/sym2021121
Received: 31 December 2009 / Revised: 14 May 2010 / Accepted: 9 June 2010 / Published: 11 June 2010
Cited by 2 | PDF Full-text (182 KB)
Abstract
This paper reviews recent approaches on how to accelerate Boolean Satisfiability (SAT) search by exploiting symmetries in the problem space. SAT search algorithms traverse an exponentially large search space looking for an assignment that satisfies a set of constraints. The presence of symmetries
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This paper reviews recent approaches on how to accelerate Boolean Satisfiability (SAT) search by exploiting symmetries in the problem space. SAT search algorithms traverse an exponentially large search space looking for an assignment that satisfies a set of constraints. The presence of symmetries in the search space induces equivalence classes on the set of truth assignments. The goal is to use symmetries to avoid traversing all assignments by constraining the search to visit a few representative assignments in each equivalence class. This can lead to a significant reduction in search runtime without affecting the completeness of the search. Full article
(This article belongs to the Special Issue Feature Papers: Symmetry Concepts and Applications)
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Open AccessReview Minimum Phi-Divergence Estimators and Phi-Divergence Test Statistics in Contingency Tables with Symmetry Structure: An Overview
Symmetry 2010, 2(2), 1108-1120; https://doi.org/10.3390/sym2021108
Received: 12 March 2010 / Revised: 7 May 2010 / Accepted: 10 June 2010 / Published: 11 June 2010
PDF Full-text (144 KB)
Abstract
In the last years minimum phi-divergence estimators (MϕE) and phi-divergence test statistics (ϕTS) have been introduced as a very good alternative to classical likelihood ratio test and maximum likelihood estimator for different statistical problems. The main purpose of this
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In the last years minimum phi-divergence estimators (MϕE) and phi-divergence test statistics (ϕTS) have been introduced as a very good alternative to classical likelihood ratio test and maximum likelihood estimator for different statistical problems. The main purpose of this paper is to present an overview of the main results presented until now in contingency tables with symmetry structure on the basis of (MϕE) and (ϕTS). Full article
(This article belongs to the Special Issue Feature Papers: Symmetry Concepts and Applications)
Open AccessArticle Fluctuating Asymmetry in Flies, What Does It Mean?
Symmetry 2010, 2(2), 1099-1107; https://doi.org/10.3390/sym2021099
Received: 23 February 2010 / Revised: 11 May 2010 / Accepted: 27 May 2010 / Published: 4 June 2010
Cited by 2 | PDF Full-text (951 KB)
Abstract
The degree of departure from perfect symmetry in organisms, fluctuating asymmetry (FA), is seen in most populations of animals. It has particular impact on choice of mate which lies within the world of sexual selection. Here I consider a relatively little studied aspect
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The degree of departure from perfect symmetry in organisms, fluctuating asymmetry (FA), is seen in most populations of animals. It has particular impact on choice of mate which lies within the world of sexual selection. Here I consider a relatively little studied aspect of sexual selection, i.e. the effect of FA on contests between males for mates, based not on display ornament but rather on agility seen in the mating systems of many insects. The model organism considered is the ubiquitous chironomid midge. In these flies, mating takes place in the air, so symmetry in the length of wings bears directly on a male’s aerobatic ability on which successful mating depends. The role of parasites and predators in creating and responding to FA in the host/prey midge is considered. Full article
(This article belongs to the Special Issue Feature Papers: Symmetry Concepts and Applications)
Open AccessReview The Relationships between Symmetry and Attractiveness and Mating Relevant Decisions and Behavior: A Review
Symmetry 2010, 2(2), 1081-1098; https://doi.org/10.3390/sym2021081
Received: 30 April 2010 / Revised: 8 May 2010 / Accepted: 24 May 2010 / Published: 26 May 2010
Cited by 9 | PDF Full-text (199 KB)
Abstract
Evolutionary theory based research shows that attractiveness is based on biological correlates that index appropriate estrogen and testosterone levels. Symmetry affects or plays a role in the perception of many of these correlates of attractiveness. Additionally, since attractiveness affects infidelity perception and reactions,
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Evolutionary theory based research shows that attractiveness is based on biological correlates that index appropriate estrogen and testosterone levels. Symmetry affects or plays a role in the perception of many of these correlates of attractiveness. Additionally, since attractiveness affects infidelity perception and reactions, sexual satisfaction, and personality perception, symmetry also affects these areas. This paper reviews the literature on symmetry showing how symmetry affects: the correlates of attractiveness, sexual satisfaction, personality, and infidelity perceptions and reactions. Full article
(This article belongs to the Special Issue Symmetry and Beauty)
Open AccessReview Photochirogenesis: Photochemical Models on the Origin of Biomolecular Homochirality
Symmetry 2010, 2(2), 1055-1080; https://doi.org/10.3390/sym2021055
Received: 1 March 2010 / Revised: 26 April 2010 / Accepted: 13 May 2010 / Published: 25 May 2010
Cited by 16 | PDF Full-text (557 KB)
Abstract
Current research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons to assume that these
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Current research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons to assume that these molecules were specific chiral amino acids. Chiral amino acids have been identified in both chondritic meteorites and simulated interstellar ices. Present research reasons that circularly polarized electromagnetic radiation was identified in interstellar environments and an asymmetric interstellar photon-molecule interaction might have triggered biomolecular symmetry breaking. We review on the possible prebiotic interaction of ‘chiral photons’ in the form of circularly polarized light, with early chiral organic molecules. We will highlight recent studies on enantioselective photolysis of racemic amino acids by circularly polarized light and experiments on the asymmetric photochemical synthesis of amino acids from only one C and one N containing molecules by simulating interstellar environments. Both approaches are based on circular dichroic transitions of amino acids that will be presented as well. Full article
(This article belongs to the Special Issue Symmetry of Life and Homochirality)
Open AccessReview Symmetry OUT, Asymmetry IN
Symmetry 2010, 2(2), 1033-1054; https://doi.org/10.3390/sym2021033
Received: 15 March 2010 / Revised: 23 April 2010 / Accepted: 18 May 2010 / Published: 25 May 2010
Cited by 2 | PDF Full-text (2461 KB)
Abstract
The formation of a perfect vertebrate body plan poses many questions that thrill developmental biologists. Special attention has been given to the symmetric segmental patterning that allows the formation of the vertebrae and skeletal muscles. These segmented structures derive from bilaterally symmetric units
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The formation of a perfect vertebrate body plan poses many questions that thrill developmental biologists. Special attention has been given to the symmetric segmental patterning that allows the formation of the vertebrae and skeletal muscles. These segmented structures derive from bilaterally symmetric units called somites, which are formed under the control of a segmentation clock. At the same time that these symmetric units are being formed, asymmetric signals are establishing laterality in nearby embryonic tissues, allowing the asymmetric placement of the internal organs. More recently, a “shield” that protects symmetric segmentation from the influence of laterality cues was uncovered. Here we review the mechanisms that control symmetric versus asymmetric development along the left-right axis among vertebrates. We also discuss the impact that these studies might have in the understanding of human congenital disorders characterized by congenital vertebral malformations and abnormal laterality phenotypes. Full article
(This article belongs to the Special Issue Feature Papers: Symmetry Concepts and Applications)
Open AccessReview Origin of Homochirality of Amino Acids in the Biosphere
Symmetry 2010, 2(2), 1022-1032; https://doi.org/10.3390/sym2021022
Received: 21 January 2010 / Revised: 28 April 2010 / Accepted: 10 May 2010 / Published: 13 May 2010
Cited by 9 | PDF Full-text (1045 KB) | Supplementary Files
Abstract
Discussions are made concerning realistic mechanisms for the origin of L-amino acids in the biosphere. As the most plausible mechanism, it is proposed that a mixture of racemic amino acids in the prebiotic sea caused spontaneous and effective optical resolution through self crystallization,
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Discussions are made concerning realistic mechanisms for the origin of L-amino acids in the biosphere. As the most plausible mechanism, it is proposed that a mixture of racemic amino acids in the prebiotic sea caused spontaneous and effective optical resolution through self crystallization, even if asymmetric synthesis of a single amino acid has never occurred without the aid of an optically active molecule. This hypothesis is based on recrystallization of a mixture of D,L-amino acids in the presence of excess of D,L-asparagine (Asn). The enantiomeric excess (ee) of each amino acid in the resulting crystals indicates that crystallization of co-existing amino acids with the configuration same as that of Asn took place, although it was incidental whether the enrichment occurred in L- or D-amino acids. In addition, the resulting ee was sufficiently high (up to 100%) to account for the predominance of L-amino acids on the earth. Full article
(This article belongs to the Special Issue Symmetry of Life and Homochirality)
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Open AccessArticle Magnetization Dynamics Symmetry in Spin Torque Induced Magnetization Switching
Symmetry 2010, 2(2), 999-1021; https://doi.org/10.3390/sym2020999
Received: 27 December 2009 / Revised: 28 April 2010 / Accepted: 30 April 2010 / Published: 7 May 2010
Cited by 1 | PDF Full-text (266 KB)
Abstract
Magnetization dynamics symmetry plays important roles in magnetization switching. Here we study magnetic field and spin torque induced magnetization switching. Spin moment transferring from polarized itinerant electrons to local magnetization provides a magnetization switching mechanism without using external magnetic field. Besides its importance
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Magnetization dynamics symmetry plays important roles in magnetization switching. Here we study magnetic field and spin torque induced magnetization switching. Spin moment transferring from polarized itinerant electrons to local magnetization provides a magnetization switching mechanism without using external magnetic field. Besides its importance in fundamental magnetization switching dynamics, spin torque magnetization switching has great application potential for future nanoscale magnetoelectronic devices. The paper explores magnetization dynamics symmetry effects on spin torque induced magnetization switching, and its interactions with random fluctuations. We will illustrate the consequences of magnetization dynamics symmetry on the critical switching current magnitude and the thermal stability energy of spin torque induced magnetization switching, which are the two most important design criteria for nanoscale spin torque magnetic devices. The concept of Logarithmic magnetization susceptibility is used to extract symmetry and damping information on spin torque induced nonlinear magnetization dynamic processes, and provides paths to control spin torque induced switching in a fluctuating environment. Full article
(This article belongs to the Special Issue Feature Papers: Symmetry Concepts and Applications)
Open AccessReview Noether Symmetries and Covariant Conservation Laws in Classical, Relativistic and Quantum Physics
Symmetry 2010, 2(2), 970-998; https://doi.org/10.3390/sym2020970
Received: 12 January 2010 / Revised: 13 April 2010 / Accepted: 21 April 2010 / Published: 29 April 2010
Cited by 2 | PDF Full-text (211 KB)
Abstract
We review the Lagrangian formulation of (generalised) Noether symmetries in the framework of Calculus of Variations in Jet Bundles, with a special attention to so-called “Natural Theories” and “Gauge-Natural Theories” that include all relevant Field Theories and physical applications (from Mechanics to General
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We review the Lagrangian formulation of (generalised) Noether symmetries in the framework of Calculus of Variations in Jet Bundles, with a special attention to so-called “Natural Theories” and “Gauge-Natural Theories” that include all relevant Field Theories and physical applications (from Mechanics to General Relativity, to Gauge Theories, Supersymmetric Theories, Spinors, etc.). It is discussed how the use of Poincar´e–Cartan forms and decompositions of natural (or gauge-natural) variational operators give rise to notions such as “generators of Noether symmetries”, energy and reduced energy flow, Bianchi identities, weak and strong conservation laws, covariant conservation laws, Hamiltonian-like conservation laws (such as, e.g., so-calledADMlaws in General Relativity) with emphasis on the physical interpretation of the quantities calculated in specific cases (energy, angular momentum, entropy, etc.). A few substantially new and very recent applications/examples are presented to better show the power of the methods introduced: one in Classical Mechanics (definition of strong conservation laws in a frame-independent setting and a discussion on the way in which conserved quantities depend on the choice of an observer); one in Classical Field Theories (energy and entropy in General Relativity, in its standard formulation, in its spin-frame formulation, in its first order formulation “à la Palatini” and in its extensions to Non-Linear Gravity Theories); one in Quantum Field Theories (applications to conservation laws in Loop Quantum Gravity via spin connections and Barbero–Immirzi connections). Full article
(This article belongs to the Special Issue Entropy, Order and Symmetry)
Open AccessReview Synthesis and Reactions of Dibenzo[a,e]pentalenes
Symmetry 2010, 2(2), 950-969; https://doi.org/10.3390/sym2020950
Received: 28 January 2010 / Revised: 11 March 2010 / Accepted: 20 April 2010 / Published: 21 April 2010
Cited by 56 | PDF Full-text (279 KB)
Abstract
Pentalene has recently received a considerable amount of attention as a ligand in sandwich-type transition metal complexes. In contrast, dibenzo[a,e]pentalene (hereafter denoted as dibenzopentalene), which is more π-extended than pentalene, has received less attention, despite its potential usefulness as a building
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Pentalene has recently received a considerable amount of attention as a ligand in sandwich-type transition metal complexes. In contrast, dibenzo[a,e]pentalene (hereafter denoted as dibenzopentalene), which is more π-extended than pentalene, has received less attention, despite its potential usefulness as a building block of ladder-type π-conjugated molecules, which have recently received growing interest. However, very recently, several novel efficient methods for the synthesis of dibenzopentalenes have been reported. This review surveys recent advances in the synthesis and reactions of dibenzopentalenes and describes the aromaticity of their ionic species. Full article
Open AccessArticle Chiroptical Properties of Amino Acids: A Density Functional Theory Study
Symmetry 2010, 2(2), 935-949; https://doi.org/10.3390/sym2020934
Received: 6 March 2010 / Revised: 6 April 2010 / Accepted: 14 April 2010 / Published: 19 April 2010
Cited by 9 | PDF Full-text (3114 KB)
Abstract
Amino acids are involved in many scientific theories elucidating possible origins of life on Earth. One of the challenges when discussing the evolutionary origin of biopolymers such as proteins and oligonucleotides in living organisms is the phenomenon that these polymers implement monomers of
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Amino acids are involved in many scientific theories elucidating possible origins of life on Earth. One of the challenges when discussing the evolutionary origin of biopolymers such as proteins and oligonucleotides in living organisms is the phenomenon that these polymers implement monomers of exclusively one handedness, a feature called biomolecular homochirality. Many attempts have been made to understand this process of racemic symmetry breaking. Assuming an extraterrestrial origin of the molecular building blocks of living organisms, their susceptibility to asymmetric photolysis by the absorption of circularly polarized electromagnetic radiation in interstellar space was proposed. In order to predict whether the interaction of circularly polarized light with various racemic amino acids can induce an enantiomeric excess, we investigated the electronic and chiroptical properties of the amino acids valine and isovaline by a molecular modelling approach based on quantum chemistry (Density Functional Theory). The average spectra of both L-valine and L-isovaline have been produced on the basis of Boltzmann population analysis using computed spectra for the various conformations of each amino acid. Full article
(This article belongs to the Special Issue Symmetry of Life and Homochirality)
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Open AccessArticle Miscellania about Entropy, Energy, and Available Free Energy
Symmetry 2010, 2(2), 916-934; https://doi.org/10.3390/sym2020916
Received: 25 February 2010 / Revised: 12 April 2010 / Accepted: 14 April 2010 / Published: 19 April 2010
Cited by 1 | PDF Full-text (556 KB)
Abstract
While the main concepts of thermodynamics are universal, the application to specific systems is not. Thus, the universal concepts combined with specific constitutive relations permit the derivation of important results in such fields as diverse as physics, chemistry, physical chemistry, chemical engineering and
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While the main concepts of thermodynamics are universal, the application to specific systems is not. Thus, the universal concepts combined with specific constitutive relations permit the derivation of important results in such fields as diverse as physics, chemistry, physical chemistry, chemical engineering and rheology. In all of these fields equilibrium is characterized either by a maximum of entropy or by a minimum of available free energies, depending on boundary data. In the latter case there is a compromise between the entropic tendency to grow and the energetic tendency to decrease. After some historical considerations the situation is illustrated for several specific cases: planetary atmospheres, osmosis and elastic rubber molecules, pertaining to physics, chemistry and rheology respectively. Afterwards, in the later parts of the article, thermodynamics considerations are extrapolated to remote fields, to wit evolutionary genetics and sociology. Full article
(This article belongs to the Special Issue Entropy, Order and Symmetry)
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