Related papers: Towards mathematical spaces for biological process…
Phase Space is the framework best suited for quantizing superintegrable systems--systems with more conserved quantities than degrees of freedom. In this quantization method, the symmetry algebras of the hamiltonian invariants are preserved…
Through extended consideration of two wide classes of case studies -- dilute gases and linear systems -- I explore the ways in which assumptions of probability and irreversibility occur in contemporary statistical mechanics, where the…
Partition logics -- non-Boolean event structures obtained by pasting Boolean algebras -- provide a natural language for situations in which a system has a definite latent state but can be accessed and resolved only through mutually…
The prediction of protein stability changes following single-point mutations plays a pivotal role in computational biology, particularly in areas like drug discovery, enzyme reengineering, and genetic disease analysis. Although…
We investigate the profound relation between the equations of biological evolution and quantum mechanics by writing a biologically inspired equation for the stochastic dynamics of an ensemble of particles. Interesting behavior is observed…
We describe a new class of models of quantum space-time based on energetic causal sets and show that under natural conditions space-time emerges from them. These are causal sets whose causal links are labelled by energy and momentum and…
An equilibrium theory of classical fluids based on the space distribution among the particles is derived in the framework of the energy minimization method. This study is motivated by current difficulties of evaluation of optical properties…
The Paradigms introduced in philosophy of science one century ago are shown to be quite more satisfactory of that introduced by Galileo. This is particularly evident in the physics based on Hilbert Spaces and related mathematical structures…
We propose a special relativistic framework for quantum mechanics. It is based on introducing a Hilbert space for events. Events are taken as primitive notions (as customary in relativity), whereas quantum systems (e.g. fields and…
Everett's Relative State Interpretation has gained increasing interest due to the progress of understanding the role of decoherence. In order to fulfill its promise as a realistic description of the physical world, two postulates are…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
Applications of quantum mechanics have led to many successful predictions and explanations of puzzling phenomena, and we now apply quantum mechanics to gain, process, and communicate information in novel ways. We can understand quantum…
The physical world is quantum. However, our description of the quantum physics still relies much on concepts in classical physics and in some cases with `quantized' interpretations. The most important case example is that of spacetime. We…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
We provide an overview of standard "projective" quantum measurements with the goal of elucidating connections between theory and experiment. We make use of a unitary "Stinespring" representation of measurements on a dilated Hilbert space…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
We propose a new systematic fibre bundle formulation of nonrelativistic quantum mechanics. The new form of the theory is equivalent to the usual one but it is in harmony with the modern trends in theoretical physics and potentially admits…
Stability landscapes are useful for understanding the properties of dynamical systems. These landscapes can be calculated from the system's dynamical equations using the physical concept of scalar potential. Unfortunately, for most…
When a system has more than one stable state, how can the stability of these states be compared? This deceptively simple question has important consequences for ecosystems, because systems with alternative stable states can undergo dramatic…
Statistical systems are conceived from the standpoint of statistical mechanics, as made of a (generally large) number of identical units and exhibiting a (generally large) number of different configurations (microstates), among which only…