Related papers: Phase Separation in Peptide Aggregation Processes …
Several neurological disorders are associated with the aggregation of aberrant proteins, often localized in intracellular organelles such as the endoplasmic reticulum. Here we study protein aggregation kinetics by mean-field reactions and…
The three species ABC model of driven particles on a ring is generalized to include vacancies and particle-nonconserving processes. The model exhibits phase separation at high densities. For equal average densities of the three species, it…
We propose a model describing the phase behavior of two-component membranes consisting of binary mixtures of electrically charged and neutral lipids. We take into account the structural phase transition (main-transition) of the hydrocarbon…
If a binary liquid mixture, composed of two alternative species with equal amounts, is quenched from a high temperature to a low temperature, below the critical point of demixing, then the mixture will phase separate through a process known…
We consider the Microcanonical Variational Principle for the vortex system in a bounded domain. In particular we are interested in the thermodynamic properties of the system in domains of second kind, i.e. for which the equivalence of…
The thermodynamics of phase transitions between phases that are size-mismatched but coherent differs from conventional stress-free thermodynamics. Most notably, in open systems such phase transitions are always associated with hysteresis.…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Self-assembly kinetics is usually described by approaches which assume that the shape of the aggregates has a definite form (e.g., spherical, cylindrical, cubic, etc), however that is unlikely to be the case in many finite-sized…
As a generic model system of an asymmetric binary fluid mixture, hexadecane dissolved in carbon dioxide is considered, using a coarse-grained bead-spring model for the short polymer, and a simple spherical particle with Lennard-Jones…
A method is presented that allows exact calculations of fragment multiplicity distributions for a canonical ensemble of non-interacting clusters. Fragmentation properties are shown to depend on only a few parameters. Fragments are shown to…
Relying on the recently proposed multicanonical algorithm, we present a numerical simulation of the first order phase transition in the 2d 10-state Potts model on lattices up to sizes $100\times100$. It is demonstrated that the new…
We describe a finite inhomogeneous three dimensional system of classical particles which interact through short and (or) long range interactions by means of a simple analytic spin model. The thermodynamic properties of the system are worked…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
A multiphysics modeling approach for heat conduction in metal hydride powders is presented, including particle shape distribution, size distribution, granular packing structure, and effective thermal conductivity. A statistical geometric…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
Soft condensed matter structures often challenge us with complex many-body phenomena governed by collective modes spanning wide spatial and temporal domains. In order to successfully tackle such problems mesoscopic coarse-grained (CG)…
The aim of this work is to study how the thermodynamic temperature is related to the known thermometers for nuclei especially in view of studying the microcanonical phase transition. We find within the MMMC-model that the "S-shape" of the…