Related papers: Crowding induced entropy-enthalpy compensation in …
The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on…
A dynamic herding model with interactions of trading volumes is introduced. At time $t$, an agent trades with a probability, which depends on the ratio of the total trading volume at time $t-1$ to its own trading volume at its last trade.…
We calculate the diffusion coefficient of an active tracer in a schematic crowded environment, represented as a lattice gas of passive particles with hardcore interactions. Starting from the master equation of the problem, we put forward a…
Entropy is a quantity for counting physical degrees of freedom in a system. At a finite temperature, one can use thermal entropy to study thermodynamical properties. At zero temperature, entanglement entropy is expected to provide a…
Recent calculations have shown that the linear proportionality between black hole entropy and area can be explained by performing a density matrix calculation for a massless free field theory. By applying the same formalism to an empirical…
An information theory model is used to construct a molecular explanation why hydrophobic solvation entropies measured in calorimetry of protein unfolding converge at a common temperature. The entropy convergence follows from the weak…
The population dynamics and stability of ecosystems of interacting species is studied from the perspective of non-equilibrium thermodynamics by assuming that species, through their biotic and abiotic interactions, are units of entropy…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
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.…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
In addition to the well known common properties such as small world and community structures, recent empirical investigations suggest a universal scaling law for the spatial structure of social networks. It is found that the probability…
We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…
Human populations exhibit complex behaviors---characterized by long-range correlations and surges in activity---across a range of social, political, and technological contexts. Yet it remains unclear where these collective behaviors come…
Population dynamics deals with the collective phenomena of living organisms, and it has attracted much attention since it is expected to explain how not only living organisms but also human beings have been adapted to varying environments.…
We present a formal treatment of the Crowd-Anticrowd theory of Minority Games played by a population of competing agents. This theory is built around a description of the crowding which arises within the game's strategy space. Earlier works…
Based on statistical mechanics, a macroscopically homogeneous system, i.e., a single phase in the present context, is composed of many independent configurations that the system embraces. The macroscopical properties of the system are…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
Schema matching is a central challenge for data integration systems. Inspired by the popularity and the success of crowdsourcing platforms, we explore the use of crowdsourcing to reduce the uncertainty of schema matching. Since…
Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the…
Using simple conditions drawn from the stability of the cosmos in terms of vacuum energy density, the cut-off momentum of entanglement is related to the planckian mass. In so doing the black hole entropy is shown to be independent of the…