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Proteins have evolved through mutations, amino acid substitutions, since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function,…
The problematic relationship between science and philosophy has, since the beginning of modernity, divided the world into two separate domains: nature and human. Some of today's schools of philosophy and epistemological inquiry have…
The main difficulty in solving the discrete constrained problem is its poor and even ill condition. In this paper, we transform the discrete constrained problems on de Rham complex to Laplace-like problems. This transformation not only make…
The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…
More than hundred years ago the 'classic physics' was it in its full power, with just a few unexplained phenomena; which however led to a revolution and the development of the 'modern physics'. Today the computing is in a similar position:…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the…
The notion of uncertainty is of major importance in machine learning and constitutes a key element of machine learning methodology. In line with the statistical tradition, uncertainty has long been perceived as almost synonymous with…
The dynamics of particles with intrinsic angular momentum (spin) described by the Dirac equation is considered in a homogeneous space with rotation in the presence of a homogeneous vortex gravitational field. The effects of the interaction…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
Molecular biology features numerous complexes of proteins that coordinate in an interlocking fashion to fulfill different functions. Adaptive evolution explains some of this complexity, but needn't be the default when neutral explanations…
For molecules and solids containing heavy elements, accurate electronic structure calculations require accounting not only for electronic correlations but also for relativistic effects. In molecules, relativity can lead to severe changes in…
The Quantum Decision Theory, developed recently by the authors, is applied to clarify the role of risk and uncertainty in decision making and in particular in relation to the phenomenon of dynamic inconsistency. By formulating this notion…
I describe my path to unconventionality in my exploration of theoretical and applied aspects of computation towards revealing the algorithmic and reprogrammable properties and capabilities of the world, in particular related to applications…
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
Integral transform approaches are numerous in many fields of physics, but in most cases limited to the use of the Laplace kernel. However, it is well known that the inversion of the Laplace transform is very problematic, so that the…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…