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Quantum theory of hydrogen atoms distribution between two complementary nucleotide bases in DNA double helix at moment of replication has been proposed in this work. It bases on two mechanisms of proton tunneling: the Andreev-Meyerovich…
A theory of electrical transport through molecular wires is used to estimate the electronic factor in the intramolecular electron transfer (ET) in porphyrin-nitrobenzene supermolecules, and to analyze its structure. The chosen molecules…
We analyze the effect of a gate on the conductance of molecules by separately evaluating the gate-induced polarization and the potential shift of the molecule relative to the leads. The calculations use ab initio density functional theory…
Water mediates a broad range of chemical reactions, including proton transfer, bond rearrangement, and conventional radical processes, defining a continuously expanding repertoire of intrinsic reactivity. However, roaming, a fundamental…
We study the dynamical behaviour of the proton transfer in the hydrogen bonds in the base-pairs of the double helices of the DNA type. Under the assumption that the elastic and the tunnelling degrees of freedom may be coupled, we derive a…
Aqueous radiation chemistry emerges through ultrafast proton transfer and ion-radical formation with unexplored energy-redistribution dynamics steering the subsequent reactions. We performed time-resolved disruptive probing on pure water…
We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores in physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl…
The electric double layer (EDL) governs electrocatalysis, energy conversion, and storage, yet its atomic structure, capacitance, and reactivity remain elusive. Here we introduce a machine learning interatomic potential framework that…
In this paper, we propose adding enzymes to the propagation environment of a diffusive molecular communication system as a strategy for mitigating intersymbol interference. The enzymes form reaction intermediates with information molecules…
Spatial organization in metabolic pathways can arise from the interplay between enzymatic reaction kinetics and diffusion-driven instabilities. In this work we investigate how reversible enzyme--substrate binding influences pattern…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
We incorporate hydrodynamic interactions in a structure-based model of ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak force when stretching the protein at constant speed, especially at larger speeds.…
Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and…
Fusion of lipid bilayers in membranes is important in processes from vesicle-cell interactions (as in drug delivery) to exosome-cell signaling, while transient transmembrane electric fields are known to occur spontaneously. Two contacting…
The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of…
The paper shows how the diffusive movement of ions through a channel protein can be described as a chemical reaction over an arbitrary shaped potential barrier. The result is simple and intuitive but without approximation beyond the…
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…
Electrostatics plays a key role in biomolecular assembly. Oppositely charged biomolecules, for instance, can co-assembled into functional units, such as DNA and histone proteins into nucleosomes and actin-binding protein complexes into…
According to the Heisenberg uncertainty principle of quantum mechanics, particles which are localized in space by a bounding potential must have a finite distribution of momenta. This leads, even in the lowest-possible energy state, to…
Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e. domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the…