Related papers: Statistical Mechanics of Integral Membrane Protein…
Protein molecules often self-assemble by means of non-covalent physical bonds to form extended filaments, such as amyloids, F-actin, intermediate filaments, and many others. The kinetics of filament growth is limited by the disassembly…
We consider the asymmetric simple exclusion process on a ring, with an arbitrary asymmetry between the hopping rates of the particles. Using a functional formulation of the Bethe equations of the model, we derive exact expressions for all…
In an adiabatically shielded system the total enthalpy is conserved. Enthalpy fluctuations of an arbitrarily chosen subsystem must be buffered by the remainder of the total system which serves as a heat reservoir. The magnitude of these…
We consider the random fluctuations of the free energy in the $p$-spin version of the Sherrington-Kirkpatrick model in the high temperature regime. Using the martingale approach of Comets and Neveu as used in the standard SK model combined…
The role of thermal pressure fluctuations in the ejection of tightly packaged DNA from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of…
We present an analysis of the role of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we compute the harmonic spectrum within the Gaussian…
It is common to study polymer physics through the use of idealized single-chain models, and the most popular of these is the freely jointed chain model. In certain thermodynamic ensembles, statistical mechanical treatment of this model is…
The ratio of the symmetry energy coefficient to temperature, $a_sym/T$, in Fermi energy heavy ion collisions, has been experimentally extracted as a function of the fragment atomic number using isoscaling parameters and the variance of the…
We discuss thermal and active fluctuations of a compressible bilayer vesicle by using the results of hydrodynamic theory for vesicles. Coupled Langevin equations for the membrane deformation and the density fields are employed to calculate…
We present a general and systematic theory of non-equilibrium dynamics of multi-component fluid membranes, in general, and membranes containing transmembrane proteins, in particular. Developed based on a minimal number of principles of…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
We measure the equation of state in a bilayer Hubbard system for different ratios of the two tunnelling amplitudes $t_\perp /t$. From the equation of state we deduce the compressibility and observe its dependency on $t_\perp /t$. Moreover,…
Understanding fluctuation-induced breakages in polymers has important implications for basic and applied sciences. Here I present for the first time an analytical treatment of the thermal breakage problem of a semi-flexible polymer model…
The potential energy landscape (PEL) of supercooled binary Lennard-Jones (BLJ) mixtures exhibits local minima, or inherent structures (IS), which are organized into meta-basins (MB). We study the particle rearrangements related to…
A central quantity in the design of functional hydrogels used as nanocarrier systems, for instance for drug delivery or adaptive nanocatalysis, is the partition ratio, which quantifies the uptake of a molecular substance by the polymer…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
We present mesoscale numerical simulations based on the coupling of the fluctuating lattice Boltzmann method (FLBM) for multicomponent systems with a wetted finite-size particle model. This newly coupled methodologies are used to study the…
An understanding of how turbulent energy is partitioned between ions and electrons in weakly collisional plasmas is crucial for modelling many astrophysical systems. Using theory and simulations of a four-dimensional reduced model of…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…