Density-Profile Processes Describing Biological Signaling Networks: Almost Sure Convergence to Deterministic Trajectories

We introduce jump processes in R(k), called density-profile processes, to model biological signaling networks. Our modeling setup describes the macroscopic evolution of a finite-size spin-flip model with k types of spins with arbitrary number of internal states interacting through a non-reversible stochastic dynamics. We are mostly interested on the multi-dimensional empirical-magnetization vector in the thermodynamic limit, and prove that, within arbitrary finite time-intervals, its path converges almost surely to a deterministic trajectory determined by a first-order (non-linear) differential equation with explicit bounds on the distance between the stochastic and deterministic trajectories. As parameters of the spin-flip dynamics change, the associated dynamical system may go through bifurcations, associated to phase transitions in the statistical mechanical setting. We present a simple example of spin-flip stochastic model, associated to a synthetic biology model known as repressilator, which leads to a dynamical system with Hopf and pitchfork bifurcations. Depending on the parameter values, the magnetization random path can either converge to a unique stable fixed point, converge to one of a pair of stable fixed points, or asymptotically evolve close to a deterministic orbit in Rk. We also discuss a simple signaling pathway related to cancer research, called p53 module.

On the Derived Categories and Quasitilted Algebras

In this paper, we present some results on the bounded derived category of Artin algebras, and in particular on the indecomposable objects in these categories, using homological properties. Given a complex X*, we consider the set J(X*) = {i is an element of Z vertical bar H(i)(X*) not equal 0} and we define the application l(X*) = maxJ(X*) - minJ(X*) + 1. We give relationships between some homological properties of an algebra and the respective application l. On the other hand, using homological properties again, we determine two subcategories of the bounded derived category of an algebra, which turn out to be the bounded derived categories of quasi-tilted algebras. As a consequence of these results we obtain new characterizations of quasi-tilted and quasi-tilted gentle algebras.

A NOTE ON THE COMPOSITE OF TWO IRREDUCIBLE MORPHISMS

In this note, we show that a composite of two irreducible morphisms between indecomposable modules cannot lie in R(3)\R(5).

Examples of Self-Iterating Lie Algebras, 2

We study properties of self-iterating Lie algebras in positive characteristic. Let R = K[t(i)vertical bar i is an element of N]/(t(i)(p)vertical bar i is an element of N) be the truncated polynomial ring. Let partial derivative(i) = partial derivative/partial derivative t(i), i is an element of N, denote the respective derivations. Consider the operators v(1) = partial derivative(1) + t(0)(partial derivative(2) + t(1)(partial derivative(3) + t(2)(partial derivative(4) + t(3)(partial derivative(5) + t(4)(partial derivative(6) + ...))))); v(2) = partial derivative(2) + t(1)(partial derivative(3) + t(2)(partial derivative(4) + t(3)(partial derivative(5) + t(4)(partial derivative(6) + ...)))). Let L = Lie(p)(v(1), v(2)) subset of Der R be the restricted Lie algebra generated by these derivations. We establish the following properties of this algebra in case p = 2, 3. a) L has a polynomial growth with Gelfand-Kirillov dimension lnp/ln((1+root 5)/2). b) the associative envelope A = Alg(v(1), v(2)) of L has Gelfand-Kirillov dimension 2 lnp/ln((1+root 5)/2). c) L has a nil-p-mapping. d) L, A and the augmentation ideal of the restricted enveloping algebra u = u(0)(L) are direct sums of two locally nilpotent subalgebras. The question whether u is a nil-algebra remains open. e) the restricted enveloping algebra u(L) is of intermediate growth. These properties resemble those of Grigorchuk and Gupta-Sidki groups.

A note on tilting sequences

We discuss the existence of tilting modules which are direct limits of finitely generated tilting modules over tilted algebras.

The bound quiver of a split extension

In this paper, we give a sufficient (which is also necessary under a compatibility hypothesis) condition on a set of arrows in the quiver of an algebra A so that A is a split extension of A/M, where M is the ideal of A generated by the classes of these arrows. We also compare the notion of split extension with that of semiconvex extension of algebras.

Some examples of nil Lie algebras

Generalizing Petrogradsky`s construction, we give examples of infinite-dimensional nil Lie algebras of finite Gelfand-Kirillov dimension over any field of positive characteristic.

ON THE COMPOSITE OF THREE IRREDUCIBLE MORPHISMS IN THE FOURTH POWER OF THE RADICAL

We study here the nonzero composite of three irreducible morphisms between indecomposable modules lying in the fourth power of the radical.

SEMIPERFECT IPRI-RINGS AND RIGHT BEZOUT RINGS

We present a survey of some results on ipri-rings and right Bezout rings. All these rings are generalizations of principal ideal rings. From the general point of view, decomposition theorems are proved for semiperfect ipri-rings and right Bezout rings.

Nil graded self-similar algebras

In [19], [24] we introduced a family of self-similar nil Lie algebras L over fields of prime characteristic p > 0 whose properties resemble those of Grigorchuk and Gupta-Sidki groups. The Lie algebra L is generated by two derivations v(1) = partial derivative(1) + t(0)(p-1) (partial derivative(2) + t(1)(p-1) (partial derivative(3) + t(2)(p-1) (partial derivative(4) + t(3)(p-1) (partial derivative(5) + t(4)(p-1) (partial derivative(6) + ...))))), v(2) = partial derivative(2) + t(1)(p-1) (partial derivative(3) + t(2)(p-1) (partial derivative(4) + t(3)(p-1) (partial derivative(5) + t(4)(p-1) (partial derivative(6) + ...)))) of the truncated polynomial ring K[t(i), i is an element of N vertical bar t(j)(p) =0, i is an element of N] in countably many variables. The associative algebra A generated by v(1), v(2) is equipped with a natural Z circle plus Z-gradation. In this paper we show that for p, which is not representable as p = m(2) + m + 1, m is an element of Z, the algebra A is graded nil and can be represented as a sum of two locally nilpotent subalgebras. L. Bartholdi [3] andYa. S. Krylyuk [15] proved that for p = m(2) + m + 1 the algebra A is not graded nil. However, we show that the second family of self-similar Lie algebras introduced in [24] and their associative hulls are always Z(p)-graded, graded nil, and are sums of two locally nilpotent subalgebras.

On the Relative Socle for Stratifying Systems

Let A be a finite dimensional k-algebra, (, ) be a stratifying system in mod(A) and F() be the class of -filtered A-modules. In this article, we give the definition and also study some of the properties of the relative socle in F(). We approach the relative socle in three ways. Namely, we view it as (1) a -semisimple subobject of M having the largest -length, (2) a maximal -semisimple subobject of M, and (3) a minimal -essential subobject of M.

Free field realizations of the elliptic affine Lie algebra sl(2, R) circle plus (Omega(R)/dR)

In this paper we construct two free field realizations of the elliptic affine Lie algebra sl(2, R) circle plus Omega(R)/dR where R = C[t. t(-1), u vertical bar u(2) = t(3) - 2bt(2) + t]. The first realization provides an analogue of Wakimoto`s construction for Affine Kac-Moody algebras, but in the setting of the elliptic affine Lie algebra. The second realization gives new types of representations analogous to Imaginary Verma modules in the Affine setting. (c) 2009 Elsevier B.V. All rights reserved.

Contravariantly finite subcategories closed under predecessors

Let A be an Artin algebra and mod A be the category of finitely generated right A-modules. We prove that an additive full subcategory C of mod A closed under predecessors is contravariantly finite if and only if its right Ext-orthogonal is covariantly finite, or if and only if the Ext-injectives in C define a cotilting module (over the support algebra of C) or, equivalently, if and only if C is the support of the representable functors given by the Ext-injectives. (C) 2009 Elsevier Inc. All rights reserved.

Introducing Undergraduate Students to Science

Understanding the scientific method fosters the development of critical thinking and logical analysis of information. Additionally, proposing and testing a hypothesis is applicable not only to science, but also to ordinary facts of daily life. Knowing the way science is done and how its results are published is useful for all citizens and mandatory for science students. A 60-h course was created to offer undergraduate students a framework in which to learn the procedures of scientific production and publication. The course`s main focus was biochemistry, and it was comprised of two modules. Module I dealt with scientific articles, and Module II with research project writing. Module I covered the topics: 1) the difference between scientific knowledge and common sense, 2) different conceptions of science, 3) scientific methodology, 4) scientific publishing categories, 5) logical principles, 6) deductive and inductive approaches, and 7) critical reading of scientific articles. Module II dealt with 1) selection of an experimental problem for investigation, 2) bibliographic revision, 3) materials and methods, 4) project writing and presentation, 5) funding agencies, and 6) critical analysis of experimental results. The course adopted a collaborative learning strategy, and each topic was studied through activities performed by the students. Qualitative and quantitative course evaluations with Likert questionnaires were carried out at each stage, and the results showed the students` high approval of the course. The staff responsible for course planning and development also evaluated it positively. The Biochemistry Department of the Chemistry Institute of the University of Sao Paulo has offered the course four times.