A coarse-grained model of the myofibril: Overall dynamics and the evolution of sarcomere non-uniformities

A theoretical framework for predicting the macroscopic behavior of a muscle myofibril based on the collective behavior of sarcomeres is presented. The analysis is accomplished by rigorously transforming the nonlinear dynamics of an assemblage of sarcomeres into a partial differential equation for the probability distribution function of sarcomere lengths in the presence of stochastic temporal fluctuations and biological variability. This enables the study of biologically relevant specimens with reasonable computational effort. The model is validated by a comparison to quantitative experimental results. Further, it reproduces experimental observations that cannot be explained by standard single sarcomere models, and provides new insights into muscle function and muscle damage during cyclic loading. We show that the accumulation of overstretched sarcomeres, which is related to muscle damage, depends on a delicate interplay between the dynamics of a large number of sarcomeres and the load characteristics, such as its magnitude and frequency. Further, we show that biological variability rather than stochastic fluctuations are the main source for sarcomere non-uniformities.     

Bounds on the global dimension of certain piecewise hereditary categories

We give bounds on the global dimension of a finite length, piecewise hereditary category in terms of quantitative connectivity properties of its graph of indecomposables.We use this to show that the global dimension of a finite-dimensional, piecewise hereditary algebra A cannot exceed 3 if A is an incidence algebra of a finite poset or more generally, a sincere algebra. This bound is tight.     

Derived Equivalences of Triangular Matrix Rings Arising from Extensions of Tilting Modules

A triangular matrix ring Λ is defined by a triplet (R,S,M) where R and S are rings and _R M _S is an S-R-bimodule. In the main theorem of this paper we show that if T _S is a tilting S-module, then under certain homological conditions on the S-module M _S , one can extend T _S to a tilting complex over Λ inducing a derived equivalence between Λ and another triangular matrix ring specified by (S′, R, M′), where the ring S′ and the R-S′-bimodule M′ depend only on M and T _S , and S′ is derived equivalent to S. Note that no conditions on the ring R are needed. These conditions are satisfied when S is an Artin algebra of finite global dimension and M _S is finitely generated. In this case, (S′,R,M′) = (S, R, DM) where D is the duality on the category of finitely generated S-modules. They are also satisfied when S is arbitrary, M _S has a finite projective resolution and Ext _S ⁿ (M _S , S) = 0 for all n > 0. In this case, (S′,R,M′) = (S, R, Hom _S (M, S)).     

How to decompose arbitrary continuous-variable quantum operations

We present a general, systematic, and efficient method for decomposing any given exponential operator of bosonic mode operators, describing an arbitrary multimode Hamiltonian evolution, into a set of universal unitary gates. Although our approach is mainly oriented towards continuous-variable quantum computation, it may be used more generally whenever quantum states are to be transformed deterministically, e.g., in quantum control, discrete-variable quantum computation, or Hamiltonian simulation. We illustrate our scheme by presenting decompositions for various nonlinear Hamiltonians including quartic Kerr interactions. Finally, we conclude with two potential experiments utilizing offline-prepared optical cubic states and homodyne detections, in which quantum information is processed optically or in an atomic memory using quadratic light-atom interactions.     

Derived Equivalence Classification of the Cluster-Tilted Algebras of Dynkin Type E

We obtain a complete derived equivalence classification of the cluster-tilted algebras of Dynkin type E. There are 67, 416, 1574 algebras in types E ₆, E ₇ and E ₈ which turn out to fall into 6, 14, 15 derived equivalence classes, respectively. This classification can be achieved computationally and we outline an algorithm which has been implemented to carry out this task. We also make the classification explicit by giving standard forms for each derived equivalence class as well as complete lists of the algebras contained in each class; as these lists are quite long they are provided as supplementary material to this paper. From a structural point of view the remarkable outcome of our classification is that two cluster-tilted algebras of Dynkin type E are derived equivalent if and only if their Cartan matrices represent equivalent bilinear forms over the integers which in turn happens if and only if the two algebras are connected by a sequence of “good” mutations. This is reminiscent of the derived equivalence classification of cluster-tilted algebras of Dynkin type A, but quite different from the situation in Dynkin type D where a far-reaching classification has been obtained using similar methods as in the present paper but some very subtle questions are still open.     

On derived equivalences of categories of sheaves over finite posets

A finite poset X carries a natural structure of a topological space. Fix a field k, and denote by D^b(X) the bounded derived category of sheaves of finite dimensional k-vector spaces over X. Two posets X and Y are said to be derived equivalent if D^b(X) and D^b(Y) are equivalent as triangulated categories.We give explicit combinatorial properties of X which are invariant under derived equivalence; among them are the number of points, the Z-congruency class of the incidence matrix, and the Betti numbers. We also show that taking opposites and products preserves derived equivalence.For any closed subset Y⊆X, we construct a strongly exceptional collection in D^b(X) and use it to show an equivalence D^b(X)?D^b(A) for a finite dimensional algebra A (depending on Y). We give conditions on X and Y under which A becomes an incidence algebra of a poset.We deduce that a lexicographic sum of a collection of posets along a bipartite graph S is derived equivalent to the lexicographic sum of the same collection along the opposite .This construction produces many new derived equivalences of posets and generalizes other well-known ones.As a corollary we show that the derived equivalence class of an ordinal sum of two posets does not depend on the order of summands. We give an example that this is not true for three summands.     

On the periodicity of Coxeter transformations and the non-negativity of their Euler forms

We show that for piecewise hereditary algebras, the periodicity of the Coxeter transformation implies the non-negativity of the Euler form. Contrary to previous assumptions, the condition of piecewise heredity cannot be omitted, even for triangular algebras, as demonstrated by incidence algebras of posets.We also give a simple, direct proof, that certain products of reflections, defined for any square matrix A with 2 on its main diagonal, and in particular the Coxeter transformation corresponding to a generalized Cartan matrix, can be expressed as , where A₊, A_- are closely associated with the upper and lower triangular parts of A.     

Biological membranes from the perspective of smart materials – A theoretical study

The unique properties and diverse functionality of biological membranes make them excellent candidates for nano-scale applications, such as sensors and actuators. Taking the view of biological membranes as smart bio-materials, we study the behavior of a simply supported beam made from a biological membrane-like material. Equilibrium configurations are derived by calculating the first variation of a generalized Helfrich energy, and their stability is examined by means of the second variation. Our numerical results demonstrate the richness of phenomena exhibited by these structures, in accordance with experimental observation of multi-component vesicles. Further, we demonstrate that the intriguing behavior of biological membrane beams, which is fundamentally different from standard beams and from standard Cahn Hilliard systems, can be utilized for actuation and sensing. For example, temperature and also pressure difference across the membrane can be indirectly measured by gauging the fluorescence intensity of the membrane components.     

A Direct Electrochemical Detection Method of Melanoma Based on Melanoma Biomarker

A new method of detecting and diagnosing melanoma based on melanoma biomarker was developed and its feasibility demonstrated. The method is based on an electrochemical biosensor platform comprised of a special biochip and device, performing a multi‐channel amperometric detection of the enzymatic activity of tyrosinase, an enzyme biomarker of melanoma. The newly developed biosensor platform is able to electrochemically detect tyrosinase activity in fresh biopsy samples. This bioelectrochemical detection method is rapid, yielding results within minutes from biopsy removal. Using “as is” biopsy samples, without pretreatment, simplifies the process, saves time and reduces cost and labor dramatically. Using modern portable microelectronics provides an accurate biomarker expression measurement at the “point of care” increasing the accessibility of new bio‐chip technologies to the public.