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Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
Many systems involve numerous interacting parts and the whole system can have properties that the individual parts do not. I take this novelty as the defining characteristic of an emergent property. Other characteristics associated with…
The physical instability of the Universe model with de Sitter beginning is proved in this article. 1. It is shown that even a small addition of ultrarelativistic matter turns the de Sitter Universe into the Universe with finite past. 2.…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
We study the protein folding problem on the base of the quantum approach we proposed recently by considering the model of protein chain with nine amino-acid residues. We introduced the concept of distance space and its projections on a…
A vast body of literature addresses the complex nature of science's reproducibility crisis. In contrast with this perceived complexity, some recent papers from the discipline of physics suggests that irreproducibility does not point to a…
We discuss theories in which the standard-model particles are localized on a brane embedded in space-time with large compact extra dimensions, whereas gravity propagates in the bulk. In addition to the ground state corresponding to a…
This work is devoted to a systematic exposition of the dynamics of a rigid body, considered as a system with kinematic constraints. Having accepted the variational problem in accordance with this, we no longer need any additional postulates…
We consider decision problems under uncertainty where the options available to a decision maker and the resulting outcome are related through a causal mechanism which is unknown to the decision maker. We ask how a decision maker can learn…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
Counterfactual explanations are widely used to interpret machine learning predictions by identifying minimal changes to input features that would alter a model's decision. However, most existing counterfactual methods have not been tested…
We discuss some aspects of the approach of the mass parameters by means of the simple cranking model. In particular, it is well known that the numerical application of this formula is often subject to ambiguities or contradictions. It is…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA…
In the theoretical biology framework one fundamental problem is the so-called error catastrophe in Darwinian evolution models. We reexamine Eigen's fundamental equations by mapping them into a polymer depinning transition problem in a…
Kinetic equations play a major rule in modeling large systems of interacting particles. Recently the legacy of classical kinetic theory found novel applications in socio-economic and life sciences, where processes characterized by large…
Since protein mutations are the main driving force of evolution at the molecular level, a proper analysis of them (and the factors controlling them) will enable us to find a response to several crucial queries in evolutionary biology. Among…
This paper is concerned with complex macroscopic behaviour arising in many-body systems through the combinations of competitive interactions and disorder, even with simple ingredients at the microscopic level. It attempts to indicate and…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
Decision-makers abhor uncertainty, and it is certainly true that the less there is of it the better. However, recognizing that uncertainty is part of the equation, particularly for deciding on environmental policy, is a prerequisite for…