Pattern analysis of the genetic code

The genetic code is examined in a new and systematic fashion: we consider the code as mapping of one finite set (the 64 codons) to another (the 20 amino acids). Given a class of mappings simpler than the actual code, we ask which mappings best approximate it. This leads to an analysis of the effects of ambiguities (codon degeneracy) in one or two positions. With the 0–1 metric (counting the amino acids as equal or not equal), the codon third base degeneracy is apparent, but the first and second positions are indistinguishable; with the integrated amino acid “distance” metric compiled by Sneath (J. Theoret. Biol. 12 (1966), 157–195), the analysis ranks the information content of the three codon positions as follows: 2nd > 1st > 3rd. We discuss possible further applications of this approach to patterns in the genetic code and other codes.     

Entropy-based evaluation function in a multi-objective approach for the investigation of the genetic code robustness

The genetic code is the interface between the genetic information stored in DNA molecules and the proteins. Considering the hypothesis that the genetic code evolved to its current structure, some researches use optimization algorithms to find hypothetical codes to be compared to the canonical genetic code. For this purpose, a function with only one objective is employed to evaluate the codes, generally a function based on the robustness of the code against mutations. Very few random codes are better than the canonical genetic code when the evaluation function based on robustness is considered. However, most codons are associated with a few amino acids in the best hypothetical codes when only robustness is employed to evaluate the codes, what makes hard to believe that the genetic code evolved based on only one objective, i.e., the robustness against mutations. In this way, we propose here to use entropy as a second objective for the evaluation of the codes. We propose a Pareto approach to deal with both objectives. The results indicate that the Pareto approach generates codes closer to the canonical genetic code when compared to the codes generated by the approach with only one objective employed in the literature.     

Inertia and eigenvalue relations between symmetrized and symmetrizing matrices for the real and the general field case

Starting from a theorem of Frobenius that every n×n matrix is the product of two symmetric ones, we study relations between the similarity invariants of a square matrix and the congruence invariants of its symmetric factors. Section 1 treats the real case, Sec. 2 the arbitrary field case, and Sec. 3 the indefinite inner product case for Krein spaces. The proofs are obtained from the real canonical pair form in Secs. 1 and 3 and from the recently found rational canonical pair form in Sec. 2, each time via combinatorial type arguments on weighted partitions of n. The resulting theorems typically give bounds for the elementary divisor structure of A in terms of the index or signature of one or both of its symmetric factors (or vice versa). Our results greatly extend and generalize the classic results of Klein, Loewy, Taussky, et al., and in Sec. 2 put new light on Waterhouse's recent characterization of hereditarily euclidean fields. A short survey on the history of the subject from the early 1800s on completes the paper.     

Quantum Groups and the Genetic Code

The quantum algebra in the limit q 0 is proposed as a symmetry algebra for the genetic code. The nucleotide triplets (codons) in the DNA chain are classified in crystal bases. This construction can be compared to the baryon classification from quarks in particle physics, one main difference being the natural order in the state constituents provided by the crystal base. An operator ensuring the correspondence between codons and amino acids is constructed from the above algebra: two codons corresponding to the same or different amino acids acquire the same or different eigenvalues respectively. Then a set of relations between the physicochemical properties of the amino acids are derived and compared with the experimental data. Correlations of the codon usage for quartets and sextets are determined, fitting naturally in the framework of this model.     

On groups acting in phase space

The problem of the motion of a material point in a central field of general type is considered. It is shown that in the infinite-dimensional group of canonical transformations which leave the Hamiltonian function invariant there are no finite-dimensional subgroups which are significantly larger than the three-dimensional group of rotations (exact formulations in Sec. 3 and Sec. 5).Translated from Matematicheskie Zametki, Vol. 5, No. 1, pp. 55–61, January, 1969.I am indebted to A. A. Kirillov for helpful discussions.     

Symmetry breaking in the genetic code: Finite groups

We investigate the possibility of interpreting the degeneracy of the genetic code, i.e., the feature that different codons (base triplets) of DNA are transcribed into the same amino acid, as the result of a symmetry breaking process, in the context of finite groups. In the first part of this paper, we give the complete list of all codon representations (64-dimensional irreducible representations) of simple finite groups and their satellites (central extensions and extensions by outer automorphisms). In the second part, we analyze the branching rules for the codon representations found in the first part by computational methods, using a software package for computational group theory. The final result is a complete classification of the possible schemes, based on finite simple groups, that reproduce the multiplet structure of the genetic code.     

Contact Systems and Corank One Involutive Subdistributions

We give necessary and sufficient geometric conditions for a distribution (or a Pfaffian system) to be locally equivalent to the canonical contact system on J ⁿ (R,R ^m ). We study the geometry of that class of systems, in particular, the existence of corank one involutive subdistributions. We also distinguish regular points, at which the system is equivalent to the canonical contact system, and singular points, at which we propose a new normal form that generalizes the canonical contact system on J ⁿ (R,R ^m ) in a way analogous to that how the Kumpera–Ruiz normal form generalizes the canonical contact system on J ⁿ (R,R), which is also called the Goursat normal form.     

Optimal charging times of a battery for memory backup

This paper considers the following charging policy for a battery to back up memories of a computer system: If the voltage of a battery is lower than a prespecified threshold level when the power is on, a battery is charged for a fixed time T. Using the probability theory, an availability of the system is derived and an optimal time T^* to maximize it is discussed. A numerical example is finally given.     

Smooth three-dimensional canonical thresholds

If X is an algebraic variety with at most canonical singularities and S is a ?-Cartier hypersurface in X, then the canonical threshold of the pair (X, S) is defined as the least upper bound of the reals c for which the pair (X, cS) is canonical. We show that the set of all possible canonical thresholds of the pairs (X, S), where X is smooth and three-dimensional, satisfies the ascending chain condition. We also derive a formula for the canonical threshold of the pair (?³, S), where S is a Brieskorn singularity.     

Classifying simple closed curve pairs in the 2-sphere and a generalization of the Schoenflies theorem

A classification theory is developed for pairs of simple closed curves (A,B) in the sphere S², assuming that A∩B has finitely many components. Such a pair of simple closed curves is called an SCC-pair, and two SCC-pairs (A,B) and (A^′,B^′) are equivalent if there is a homeomorphism from S² to itself sending A to A^′ and B to B^′. The simple cases where A and B coincide or A and B are disjoint are easily handled. The component code is defined to provide a classification of all of the other possibilities. The component code is not uniquely determined for a given SCC-pair, but it is straightforward that it is an invariant; i.e., that if (A,B) and (A^′,B^′) are equivalent and C is a component code for (A,B), then C is a component code for (A^′,B^′) as well. It is proved that the component code is a classifying invariant in the sense that if two SCC-pairs have a component code in common, then the SCC-pairs are equivalent. Furthermore code transformations on component codes are defined so that if one component code is known for a particular SCC-pair, then all other component codes for the SCC-pair can be determined via code transformations. This provides a notion of equivalence for component codes; specifically, two component codes are equivalent if there is a code transformation mapping one to the other. The main result of the paper asserts that if C and C^′ are component codes for SCC-pairs (A,B) and (A^′,B^′), respectively, then (A,B) and (A^′,B^′) are equivalent if and only if C and C^′ are equivalent. Finally, a generalization of the Schoenflies theorem to SCC-pairs is presented.     

LEGENDRE TRANSFORMATIONS AND CARTAN FORMS IN THE CALCULUS OF VARIATIONS OF MULTIPLE INTEGRALS

ABSTRACT

(PART II): In terms of a given Hamiltonian function the 1-form w = dH + ?_j|dπ^j is defined, where {?_j:j = 1,…, n} denotes an invariant basis of the planes of the distribution D_n. The latter is said to be canonical if w = 0 (which is analogous to the definition of Hamiltonian vector fields in symplectic geometry). This condition is equivalent to two sets of canonical equations that are expressed explicitly in term of the derivatives of H with respect to its positional arguments. The distribution D_n is said to be pseudo-Lagrangian if dπ^j(?_j,V_h) = 0; if D_n, is both canonical and pseudo-Lagrangian it is integrable and such that H = const. on each leaf of the resulting foliation. The Cartan form associated with this construction [9] is defined a II = π² ? ? πⁿ. If π is closed, the distribution D_N is integrable, and the exterior system {π^j} admits the representation ψ^j = dS^j in terms of a set of 0-forms S^j on M. If, in addition, the distribution D_N is canonical, these functions satisfy a single first order Hamilton-Jacobi equation, and conversely. Finally, a complete figure is constructed on the basis of the assumptions that (i) the Cartan form be closed, and (ii) that the distribution D_n, be both canonical and integrable. The last of these requirements implies the existence of N functions ψ^A that depend on x^h and N parameters w^B, whose derivatives are given by ?ψ^A (x^h, w^B)/?x^j = B^A _j (x^h, ψ^B (x^h,w^B)). The complete figure then consists of two complementary foliations: the leaves of the first are described by the functions ψ^A and satisfy the standard Euler-Lagrange equations, while the second, that is, the transversal foliation, is represented by the aforementioned solution of the Hamilton-Jacobi equation. The entire configuration then gives rise in a natural manner to a generalized Hilbert independent integral and consequently also to a generalized Weierstrass excess function.     

The crystal and molecular structure of 3, 4-dihydroxy L-phenyl-alanine

The molecule crystallizes in spacegroup P2₁ with two molecules per unit cell. The unit cell dimensions area = 6.044 Å,b = 13.607 Å,c = 5.311 Å,γ = 97.55°. The density was calculated to be 1.512 g.ml.^?1 and found to be 1.51 g.ml.^?1 The major atoms were located by the reliable image method and the hydrogen atoms were located from a difference electron density map. Full-matrix least squares refinement of the parameters yielded an unweighted residual indexR of 0.088. The bond lengths and angles of the amino acid grouping are consistent with values in other amino acids. The structural parameters of the aromatic system are very similar to those of noradrenaline and dopamine hydrochlorides. The crystal structure is dominated by a three-dimensional intermolecular hydrogen bonding system. The molecular conformation is different from that displayed by any other aromatic amino acid or peptide whose crystal structure is known.     

On the semiring of cone preserving maps

If K is a proper cone in Rⁿ, then the cone of all linear operators that preserve K, denoted by π(K), forms a semiring under usual operator addition and multiplication. Recently J.G. Horne examined the ideals of this semiring. He proved that if K₁, K₂ are polyhedral cones such that π(K₁) and π(K₂) are isomorphic as semirings, then K₁ and K₂ are linearly isomorphic. The study of this semiring is continued in this paper. In Sec. 3 ideals of π(K) which are also faces are characterized. In Sec. 4 it is shown that π(K) has a unique minimal two-sided ideal, namely, the dual cone of π(K¹), where K¹ is the dual cone of K. Extending Horne's result, it is also proved that the cone K is characterized by this unique minimal two-sided ideal of π(K). The set of all faces of π(K) inherits a quotient semiring structure from π(K). Properties of this face-semiring are given in Sec. 5. In particular, it is proved that this face-semiring admits no nontrivial congruence relation iff the duality operator of π(K) is injective. In Sec. 6 the maximal one-sided and two-sided ideals of π(K) are identified. In Sec. 8 it is shown that π(K) never satisfies the ascending-chain condition on principal one-sided ideals. Some partial results on the question of topological closedness of principal one-sided ideals of π(K) are also given.     

Existence of log canonical closures

Let f:X→U be a projective morphism of normal varieties and (X,Δ) a dlt pair. We prove that if there is an open set U ⁰?U, such that (X,Δ)× _U U ⁰ has a good minimal model over U ⁰ and the images of all the non-klt centers intersect U ⁰, then (X,Δ) has a good minimal model over U. As consequences we show the existence of log canonical compactifications for open log canonical pairs, and the fact that the moduli functor of stable schemes satisfies the valuative criterion for properness.     

Mean convex hulls and least area disks spanning extreme curves

We show that for any extreme curve in a 3-manifold M, there exist a canonical mean convex hull containing all least area disks spanning the curve. Similar result is true for asymptotic case in such that for any asymptotic curve , there is a canonical mean convex hull containing all minimal planes spanning Γ. Applying this to quasi-Fuchsian manifolds, we show that for any quasi-Fuchsian manifold, there exist a canonical mean convex core capturing all essential minimal surfaces. On the other hand, we also show that for a generic C³-smooth curve in the boundary of C³-smooth mean convex domain in ℝ³, there exist a unique least area disk spanning the curve.     

Invariant functions of the elements of the powers of a square matrix

A square matrix A is raised to any real power n, negative or fractional values being permitted when Aⁿ can be defined; C is a matrix that commute with A. Linear identities existing between the elements of Aⁿ or C are investigated, in such a way that the number of elements in each identity is minimized in general. Both this number and the method of investigation depend on the Jordan canonical form of A, but if A has a special property, some of these identities and their method of derivation are independent of the Jordan canonical form.     

The solution of the equation AX + BX ⋆ = 0

We give a complete solution of the matrix equation AX?+?BX ^??=?0, where A, B?∈?? ^m×n are two given matrices, X?∈?? ^n×n is an unknown matrix, and ? denotes the transpose or the conjugate transpose. We provide a closed formula for the dimension of the solution space of the equation in terms of the Kronecker canonical form of the matrix pencil A?+?λB, and we also provide an expression for the solution X in terms of this canonical form, together with two invertible matrices leading A?+?λB to the canonical form by strict equivalence.     

The information cocycle andɛ-bounded codes

We shall prove here that Bowen’s bounded codes lead to a cocycle-coboundary equation which can be exploited in various ways: through central limit theorems, through the related information variance or through a certain group invariant. Another result which emerges is that it is impossible to boundedly code two Markov automorphisms when one is of maximal type and the other is not. The functions which appear in the above cited cocycle-coboundary equation may belong to variousL ^p spaces. We devote a section to this problem. Finally we show that the information cocycle associated with small smooth partitions of aC ² Anosov diffeomorphism preserving a smooth probability is, in a sense, canonical.     

Algebraic signatures of convex and non-convex codes

A convex code is a binary code generated by the pattern of intersections of a collection of open convex sets in some Euclidean space. Convex codes are relevant to neuroscience as they arise from the activity of neurons that have convex receptive fields. In this paper, we develop algebraic methods to determine if a code is convex. Specifically, we use the neural ideal of a code, which is a generalization of the Stanley–Reisner ideal. Using the neural ideal together with its standard generating set, the canonical form, we provide algebraic signatures of certain families of codes that are non-convex. We connect these signatures to the precise conditions on the arrangement of sets that prevent the codes from being convex. Finally, we also provide algebraic signatures for some families of codes that are convex, including the class of intersection-complete codes. These results allow us to detect convexity and non-convexity in a variety of situations, and point to some interesting open questions.     

Adjoints and pluricanonical adjoints to an algebraic hypersurface

. We develop the theory of canonical and pluricanonical adjoints, of global canonical and pluricanonical adjoints, and of adjoints and global adjoints to an irreducible, algebraic hypersurface V?? ⁿ , under certain hypotheses on the singularities of V. We subsequently apply the results of the theory to construct a non-singular threefold of general type X, desingularization of a hypersurface V of degree six in ?⁴, having the birational invariants q ₁=q ₂=p _g =0, P ₂=P ₃=5. We demonstrate that the bicanonical map ? _|2KX| is birational and finally, as a consequence of the Riemann–Roch theorem and vanishing theorems, we prove that any non-singular model Y, birationally equivalent to X, has the canonical divisors K _Y that do not (simultaneously) satisfy the two properties: (K _Y ³)>0 and K _Y numerically effective.