Related papers: Cooperativity, Absolute Interaction, and Algebraic…
An optimization technique is used to determine the pairwise interactions between amino acids in globular proteins. A numerical strategy is applied to a set of proteins for maximizing the native fold stability with respect to alternative…
Recently, we have developed an efficient generic partition refinement algorithm, which computes behavioural equivalence on a state-based system given as an encoded coalgebra, and implemented it in the tool CoPaR. Here we extend this to a…
Let $\mathbf{B}$ be a basis for an $r$-dimensional algebra $A$ over a field or commutative ring with unity. The semifusions of $\mathbf{B}$ are the partitions of $\mathbf{B}$ whose characteristic functions form the basis of a subalgebra of…
We demonstrate a cooperative optical non-linearity caused by dipolar interactions between Rydberg atoms in an ultra-cold atomic ensemble. By coupling a probe transition to the Rydberg state we map the strong dipole-dipole interactions…
We consider perturbations of dynamical semigroups on the algebra of all bounded operators in a Hilbert space generated by covariant completely positive measures on the semi-axis. The construction is based upon unbounded linear perturbations…
The duality between partial actions (partial $H$-module algebras) and co-actions (partial $H$-comodule algebras) of a Hopf algebra $H$ is fully explored in this work. A connection between partial (co)actions and Hopf algebroids is…
We introduce a general physical formulation that allows one to obtain uniquely the effectiveinteractions by contracting the bare forces, even in highly concentrated systems. We tested it bystudying depletion forces in two-dimensional binary…
Given a C*-algebra B, a closed *-subalgebra A contained in B, and a partial isometry S in B which "interacts" with A in the sense that S*aS = H(a)S*S and SaS* = V(a)SS*, where V and H are positive linear operators on A, we derive a few…
This research started with an algebra for reasoning about rely/guarantee concurrency for a shared memory model. The approach taken led to a more abstract algebra of atomic steps, in which atomic steps synchronise (rather than interleave)…
Multiagent systems can use commitments as the core of a general coordination infrastructure, supporting both cooperative and non-cooperative interactions. Agents whose objectives are aligned, and where one agent can help another achieve…
Cells constantly need to monitor the state of the environment to detect changes and timely respond. The detection of concentration changes of a ligand by a set of receptors can be cast as a problem of hypothesis testing, and the cell viewed…
Cooperative optimization is a new way for finding global optima of complicated functions of many variables. It has some important properties not possessed by any conventional optimization methods. It has been successfully applied in solving…
Inspired by regularization techniques in statistics and machine learning, we study complementary composite minimization in the stochastic setting. This problem corresponds to the minimization of the sum of a (weakly) smooth function endowed…
Differential positivity and K-cooperativity, a special case of differential positivity, extend differential approaches to control to nonlinear systems with multiple equilibria, such as switches or multi-agent consensus. To apply this…
Alignment interactions in active matter are typically modeled as relaxational dynamics toward local consensus. In unbounded systems, this makes alignment effectively decoupled from local density and therefore unable to sustain self-confined…
The minimal 3-state scheme of kinetic cooperativity of monomeric enzymes is subjected to detailed analysis. The rigorous criteria of positive cooperativity and its sigmoidal version are established in terms of the system parameters (rate…
The analysis of contingency tables is a powerful statistical tool used in experiments with categorical variables. This study improves parts of the theory underlying the use of contingency tables. Specifically, the linkage disequilibrium…
We present a new high-performance configuration interaction code optimally designed for the calculation of the lowest energy eigenstates of a few electrons in semiconductor quantum dots (also called artificial atoms) in the strong…
The classical alternating minimization (or projection) algorithm has been successful in the context of solving optimization problems over two variables. The iterative nature and simplicity of the algorithm has led to its application to many…
A quantitative model of concurrent interaction is introduced. The basic objects are linear combinations of partial order relations, acted upon by a group of permutations that represents potential non-determinism in synchronisation. This…