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The correct use and interpretation of models depends on several steps, two of which being the calibration by parameter estimation and the analysis of uncertainty. In the biological literature, these steps are seldom discussed together, but…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
Considered typical processes of rod bending under strong longitudinal compression. The dynamic equation of bending correspponds to a perturbation of the two- dimensional Laplace equation. It is established that, for these processes,…
The concept of uncertainty quanta for a general system is introduced and applied to some important problems in physics and mathematics. EPR paradox gives new clue to the further understanding of particle correlation which turns out to be…
Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…
We give an argument that a broad class of geometric models of spinning relativistic particles with Casimir mass and spin being separately fixed parameters, have indeterminate worldline (while other spinning particles have definite…
The Heisenberg position-momentum uncertainty principle shares with the equivalence principle the role of main pillar of our current description of nature. However, in its original formulation it is inconsistent with special relativity, and…
Soft colloids allow to explore high density states well beyond random close packing. An important open question is whether softness controls the dynamics under these dense conditions. While experimental works reported conflicting results,…
A long-standing tradition, largely present in both the physical and the philosophical literature, regards the advent of (special) relativity -- with its block-universe picture -- as the failure of any indeterministic program in physics. On…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
The process of doing Science in condition of uncertainty is illustrated with a toy experiment in which the inferential and the forecasting aspects are both present. The fundamental aspects of probabilistic reasoning, also relevant in real…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
The phenomenon of crumpling is common in our daily life and nature. It exhibits many interesting properties, such as ultra-tough resistance to pressure with less than 30$\%$ of volume density, power-law relation for pressure vs density, and…
The role of the Uncertainty Principle is examined through the examples of squeezing, information capacity, and position monitoring. It is suggested that more attention should be directed to conceptual considerations in quantum information…
Throughout this book, we discuss some open problems in various branches of science, including mathematics, theoretical physics, astro-physics, geophysics etc. It is of our hope that some of the problems discussed in this book will find…
The problem of the determinism of Quantum Mechanics has been a main one during the 20th century. At the same time, in the context of Logic and Set Theory, the importance of ancient paradoxes as well as the appearance of many new ones, has…
In the presence of model risk, it is well-established to replace classical expected values by worst-case expectations over all models within a fixed radius from a given reference model. This is the "robustness" approach. We show that…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…