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By molecular dynamics simulation, discovered is a strange rigid-like nature for a hexagonally packed domain of short chain molecules. In spite of the non-bonded short-range interaction potential (Lennard-Jones potential) among chain…
Many open problems in biology, as in the physical sciences, display nonlinear and 'chaotic' dynamics, which, to the extent possible, cannot be reasonably understood. Moreover, mathematical models which aim to predict/estimate unknown…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
The quantum motion of nuclei, generally ignored in sliding friction, can become important for an atom, ion, or light molecule sliding in an optical lattice. The density-matrix-calculated evolution of a quantum Prandtl-Tomlinson model,…
The use of science for policy is at the core of a perfect storm generated by the insurgence of several concurrent crises: of science, of trust, of sustainability. The modern positivistic model of science for policy, known as evidence based…
The Levinthal paradox exposes many critical questions on the protein folding problem, among which we could point out why proteins can reach their native state in a biologically reasonable time. A proper answer to this question is of…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
An analytical characterization of thermodynamically rational agent behaviour is obtained for a simple, yet non--trivial example of a ``Maxwell's demon" operating with partial information. Our results provide the first fully transparent…
The accelerating expansion of the universe presents an exciting, fundamental challenge to the standard models of particle physics and cosmology. I highlight some of the outstanding challenges in both developing theoretical models and…
We apply two theoretical and two numerical methods to the problem of a disk placed in a groove and subjected to gravity and a torque. Methods assuming rigid particles are indeterminate -- certain combinations of forces cannot be calculated,…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from…
The compactness phenomenon is one of the featured aspects of structuralism in mathematics. In simple and broad words, a compactness property holds in a structure if a related property is satisfied by sufficiently many substructures of that…
We explicitly show the connection between the protein folding problem and spin glass transition. This is then used to identify appropriate quantities that are required to describe the transition. A possible way of observing the spin glass…
Many of the concepts which are at the basis of the development associated with a quantitative treatment of the variety of phenomena associated with the spontaneous breaking of gauge symmetry in nuclei have been instrumental in connection…
With the help of lattice Monte Carlo modelling of heteropolymers, we show that the necessary condition for a protein to fold on short call is to proceed through partially folded intermediates. These elementary structures are formed at an…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
A major challenge of interdisciplinary description of complex system behaviour is whether real systems of higher complexity levels can be understood with at least the same degree of objective, "scientific" rigour and universality as…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Recent cosmological observations strongly suggest that the universe is dominated by an unknown form of energy with negative pressure. Why is this dark energy density of order the critical density today? We propose that the dark energy has…