Related papers: The Allosteric Switching Mechanism in Bacteriophag…
Minimal energy shapes of closed, elastic shells with twelve pentagonal disclinations introduced in otherwise hexagonally coordinated crystalline lattice are studied. The geometry and the total energy of shells are studied as a function of…
The unique structural properties of interfacial water are at the heart of a vast range of important processes in electrochemistry, climate science, and biophysics. At interfaces, water molecules exhibit preferential orientations and an…
Here we study the resistive switching (RS) effect that emerges when ferroelectric BaTiO$_{3}$ (BTO) and few-layers MoSe$_{2}$ are combined in one single structure. The C-V loops reveal the ferroelectric nature of both Al/Si/SiO$_{x}$/BTO/Au…
The importance of mutator clones in the adaptive evolution of asexual populations is not fully understood. Here we address this problem by using an ab initio microscopic model of living cells, whose fitness is derived directly from their…
We study the binding of plant hormone IAA on its receptor TIR1 introducing a novel computational method that we call tomographic docking and that accounts for interactions occurring along the depth of the binding pocket. Our results suggest…
ATPases cyclically convert chemical energy in the form of ATP gradients into directed motion inside cells. To function, ATPases rely on allosteric communication between at least two binding sites, an internal signaling mechanism that is not…
Allostery commonly refers to the mechanism that regulates protein activity through the binding of a molecule at a different, usually distal, site from the orthosteric site. The omnipresence of allosteric regulation in nature and its…
We aim to identify the control principles governing the adaptable formation of non-equilibrium structures in actomyosin networks. We build a phenomenological model and predict that biasing the energy dissipated by molecular motors should…
The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids according to their chemical properties during the branching…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
Deposition of MoS2 on (111)-Au alters the electronic properties of MoS2. In this study, we investigate the free-standing MoS2 monolayer and the MoS2~\(111)-Au heterostructure, with and without strain, as well as defects of interest in…
The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds…
In this work we report on the role of ion transport for the dynamic behavior of a double barrier quantum mechanical Al/Al$_2$O$_3$/Nb$_{\text{x}}$O$_{\text{y}}$/Au memristive device based on numerical simulations in conjunction with…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
On the spin-valve-like ferromagnet/spin glass/ferromagnet (FM/SG/FM) structure, the tunneling current is dominated by resistance switch (RS) instead of the local density of states according to the conventional tunneling theory. Here we show…
The anisotropic feature of charge transfer reactions in realistic proteins cannot be ignored, due to the highly complex chemical structure of bio-molecules. In this work, we have performed the first large-scale quantitative assessment of…
Despite the absence of a membrane-enclosed nucleus, the bacterial DNA is typically condensed into a compact body - the nucleoid. This compaction influences the localization and dynamics of many cellular processes including transcription,…
Two special dynamical transitions of universal character have been recently observed in macromolecules at $T_{D}\sim 180 - 220$ K and $T^{*}\sim 100$ K. Despite their relevance, a complete understanding of the nature of these transitions…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
Collective cell migration governs a range of physiological and pathological processes, from tissue morphogenesis to cancer invasion, in which topological defects arise as an inevitable consequence of frequent cellular rearrangement and…