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Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not…
A key problem of eukaryotic cell motility is the signaling mechanism of chemoattractant gradient sensing. Recent experiments have revealed the molecular correlate of gradient sensing: Frontness molecules, such as PI3P and Rac, localize at…
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…
In a 2018 paper and a subsequent article published in 2023, researchers reported that mitochondria maintain temperatures 10-15 degrees celsius higher than the surrounding cytoplasm - a finding that deviates by 5 to 6 orders of magnitude…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
This paper proposes a unified gas-kinetic particle (UGKP) method for the frequency-dependent photon transport process. The photon transport is a typical multiscale process governed by the nonlinear radiative transfer equations (RTE). The…
A model of a multilayer device with non-trivial geometrical structure and nonlinear dependencies of thermodynamic material properties at cryogenic temperatures is suggested. A considered device, called cryogenic cell, is intended for use in…
We examine a simple model of proton pumping through the inner membrane of mitochondria in the living cell. We demonstrate that the pumping process can be described using approaches of condensed matter physics. In the framework of this…
Interactions between proteins and their solvent environment can be studied in a bottom-up approach using hydrogen-bonded chromophore-solvent clusters. The ultrafast dynamics following UV-light-induced electronic excitation of the…
A phenomenological model for the unbinding transition of multi-component fluid membranes is proposed, where the unbinding transition is described using a theory analogous to Flory-Huggins theory for polymers. The coupling between the…
The thermalization of an isolated quantum system is described by quantum mechanics and thermodynamics, while these two subjects are still not fully consistent with each other. This leaves a less-explored region where both quantum and…
While generating ultracold plasma (UCP) by photoinization of laser-cooled atoms, only a small fraction of atoms are ionized, and the remaining neutrals interact with the electrons present therein. These interactions, in addition to the…
The unified gas-kinetic wave-particle method (UGKWP) has been developed for the multiscale gas, plasma, and multiphase flow transport processes for the past years. In this work, we propose an implicit unified gas-kinetic wave-particle…
The paper is devoted to a systematic account of the theory of conformational dynamics of protein molecules. As an example of application of this theory, we provide a complete analytical description of experiments on the kinetics of CO…
In this work, we present a unified gas-kinetic particle (UGKP) method for the simulation of multiscale photon transport. The multiscale nature of the particle method mainly comes from the recovery of the time evolution flux function in the…
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.…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
It was once purported that biological systems were far too warm and wet to support quantum phenomena mainly due to thermal effects disrupting quantum coherence. However recent experimental results and theoretical analyses have shown that…
We propose a scenario for the prebiotic co-evolution of RNA and of fast folding proteins with large entropy gaps as observed today. We show from very general principles that the folding and unfolding of the proteins synthesized by RNA can…
The expression for the higher temperature dependence of the mean squared displacement in proteins is obtained. The quantum multi-well model explains the dynamic transitions of the proteins and minimizes the amount of parameters to a single…