Related papers: Kinetic energy flows in activated dynamics of biom…
In processes when particles such as nanodroplets, clusters, or molecules move through a dilute background gas and undergo capture collisions, it is often important to know how much translational kinetic energy is deposited into the…
The work is presented, leading to the universal contact molecular mechanism of phase transitions and other reactions in solid state. The two components of the mechanism - nucleation and interface propagation - are investigated in detail and…
This work presents a tentative discussion of certain aspects of energy behavior in the context of mathematical fluid dynamics. While some observations are made regarding certain patterns in energy behavior under particular conditions, the…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
For a 2-dimensional freely jointed chain with 3 particles and a related model, the average and variance of the kinetic energies of each particle in thermal equilibrium are exactly obtained. The same is done for a related model. The excess…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
A study is made of how active membrane proteins can modify the long wavelength mechanics of fluid membranes. The activity of the proteins is modelled as disturbing the protein surroundings through non-local force distributions of which a…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
The surprising manifestation of collectivity in small collision systems, such as nucleon-nucleon and nucleon-nucleus collisions, is perhaps even more striking when discussed at higher momenta. In larger systems, high-$p_T$ elliptic…
We present experimental evidence for a double cascade of kinetic energy in a statistically stationary rotating turbulence experiment. Turbulence is generated by a set of vertical flaps which continuously injects velocity fluctuations…
Cells move by run and tumble, a kind of dynamics in which the cell alternates runs over straight lines and re-orientations. This erratic motion may be influenced by external factors, like chemicals, nutrients, the extra-cellular matrix, in…
Mobile microscopic bodies, such as motile cells, can be modelled phenomenologically as ``active particles'' which can move against external forces by depleting an internal energy depot. The microscopic mechanisms underlying such ``active''…
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…
Photoactive proteins absorb light and undergo structural changes that enable them to perform essential biological functions. These proteins are critical for understanding light-induced biological processes, making them important in…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
We show that transport in the presence of entropic barriers exhibits peculiar characteristics which makes it distinctly different from that occurring through energy barriers. The constrained dynamics yields a scaling regime for the particle…
We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting…
We study vibrated granular media, investigating each of the three components of the energy flow: particle-particle dissipation, energy input at the vibrating wall, and particle-wall dissipation. Energy dissipated by interparticle collisions…
Understanding how transcription factors (TFs) regulate mammalian gene expression in space and time is a central topic in biology. To activate a gene, a TF has first to diffuse in the available space of the nucleus until it reaches a target…