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Spintronics logic devices based on majority gates formed by atomic-level arrangements of spins in the crystal lattice is considered. The dynamics of switching is modeled by time-dependent solution of the density-matrix equation with…
Experimental and theoretical analyses of the lactate dehydrogenase and glutathione reductase based enzymatic AND logic gates in which the enzymes and their substrates serve as logic inputs are performed. These two systems are examples of…
Recent theoretical research has shown that self-adjusting and self-adaptive mechanisms can provably outperform static settings in evolutionary algorithms for binary search spaces. However, the vast majority of these studies focuses on…
The critical behavior of the non-diffusive susceptible-infected-recovered model on lattices had been well established in virtue of its duality symmetry. By performing simulations and scaling analyses for the diffusive variant on the…
Biological systems organize into hierarchies to manage complexity, yet the mechanisms governing hierarchical control remain incompletely understood. Using information theory and the Lambda phage lysis-lysogeny decision as a model system, we…
We summarize a recent study of discrete (integer-valued) Hamiltonian cellular automata (CA) showing that their dynamics can only be consistently defined, if it is linear in the same sense as unitary evolution described by the Schr\"odinger…
The central question of systems biology is to understand how individual components of a biological system such as genes or proteins cooperate in emerging phenotypes resulting in the evolution of diseases. As living cells are open systems in…
Bio-digital systems that merge microbial life with technology promise new modes of computation, combining biological adaptability with digital precision. Yet realizing this potential symbiotically -- where biological and digital agents…
We study unimodular transformations of conservative $L$-systems. Classes $\sM^Q$, $\sM^Q_\kappa$, $\sM^{-1,Q}_\kappa$ that are impedance functions of the corresponding $L$-systems are introduced. A unique unimodular transformation of a…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
LLMs for clinical decision support often fail under small but clinically meaningful input shifts such as masking a symptom or negating a finding, despite high performance on static benchmarks. These reasoning failures frequently go…
Branching processes in a varying environment encompass a wide range of stochastic demographic models, and their complete understanding in terms of limit behaviour poses a formidable research challenge. In this paper, we conduct a thorough…
Open quantum many-body systems with controllable dissipation can exhibit novel features in their dynamics and steady states. A paradigmatic example is the dissipative transverse field Ising model. It has been shown recently that the steady…
The Lamb shift, an energy shift arising from the presence of the electromagnetic vacuum, has been observed in various quantum systems and established as the part of the energy shift independent of the environmental photon number. However,…
We propose a hybrid dynamical system approach to model the evolution of a pathogen that experiences different selective pressures according to a stochastic process. In every environment, the evolution of the pathogen is described by a…
Genetic mutations frequently disrupt protein structure, stability, and solubility, acting as primary drivers for a wide spectrum of diseases. Despite the critical importance of these molecular alterations, existing computational models…
Soft slender structures are ubiquitous in natural and artificial systems and can be observed at scales that range from the nanometric to the kilometric, from polymers to space tethers. We present a practical numerical approach to simulate…
We consider a mechanism for area preserving Hamiltonian systems which leads to the enhanced probability, $P(\lambda, t)$, to find small values of the finite time Lyapunov exponent, $\lambda$. In our investigation of chaotic dynamical…
Modern computer systems are highly configurable, with the total variability space sometimes larger than the number of atoms in the universe. Understanding and reasoning about the performance behavior of highly configurable systems, over a…
Based on our physical and biological studies we have recently developed a mathematical framework for the analysis of nonlnear dynamics. We call this framework the dynamical structure analysis. It has four dynamical elements: potential…