Related papers: Free energy approach to micellization and aggregat…
Active particles contain internal degrees of freedom with the ability to take in and dissipate energy and, in the process, execute systematic movement. Examples include all living organisms and their motile constituents such as molecular…
We investigate the ground states of a free energy functional on sphere. The energy consists of an entropy and a nonlocal interaction term that are in competition with each other, as they favour spreading and aggregation, respectively.…
The ideas of thermodynamics have proved fruitful in the setting of quantum information theory, in particular the notion that when the allowed transformations of a system are restricted, certain states of the system become useful resources…
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…
We prove the existence of non-trivial global minimizers of a class of free energies related to aggregation equations with degenerate diffusion on $\Real^d$. Such equations arise in mathematical biology as models for organism group dynamics…
We investigate the effect of linear diffusion and interactions with the domain boundary on swarm equilibria by analyzing critical points of the associated energy functional. Through this process we uncover two properties of energy…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
The free energy of barium titanate is computed around the Curie temperature as a function of polarization from the first-principles derived effective hamiltonian of Zhong, Vanderbilt and Rabe [Phys. Rev. Lett. 73, 1861 (1994)], through…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
To understand the physics of solar flares, including the local reorganisation of the magnetic field and the acceleration of energetic particles, we have first to estimate the free magnetic energy available for such phenomena, which can be…
The proposed method of the free energy calculation is based on the approximation of the energy distribution in the microcanonical ensemble by the Gaussian distribution. We hope that our approach will be effective for the systems with…
Nonequilibrium thermodynamics formalism is proposed to derive the flux of grainy (bubbles-containing) matter, emerging in a nucleation growth process. Some power and non-power limits, due to the applied potential as well as owing to basic…
We present a simulation technique to evaluate the most important quantity for nucleation processes: the nucleation barrier, i.e. the free energy of formation of the critical cluster. The method is based on stabilizing a small cluster by…
Free energies of molecules can be calculated by quantum computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic…
We develop a systematic procedure to approximate generalized free energy in out of equilibrium stochastic systems. The procedure only requires knowledge of the averages of macroscopic observables and uses quasi-equilibrium distribution to…
The recently proposed Einstein molecule approach is extended to compute the free energy of molecular solids. This method is a variant of the Einstein crystal method of Frenkel and Ladd[J. Chem. Phys. 81,3188 (1984)]. In order to show its…
A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used,…
Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
We study the nucleation of crystalline cluster phases in the generalized exponential model with exponent n=4. Due to the finite value of this pair potential for zero separation, at high densities the system forms cluster crystals with…