Related papers: Statistical Mechanics of Integral Membrane Protein…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
Feebly Interacting Massive Particles (FIMPs) are dark matter candidates that never thermalize in the early universe and whose production takes place via decays and/or scatterings of thermal bath particles. If FIMPs interactions with the…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
Microphase separation of membrane components is thought to play an important role in many physiological processes, from cell signaling to endocytosis and cellular trafficking. Here, we study how variations in the membrane composition can be…
We numerically simulate a thermalization process in an energy landscape with hierarchically organized metastable states. The initial configuration is chosen to have a large energy excess, relative to the thermal equilibrium value at the…
We investigate the properties of membranes under tension by Monte-Carlo simulations of a generic coarse-grained model for lipid bilayers. We give a comprising overview of the behavior of several membrane characteristics, such as the area…
The one-dimensional totally asymmetric simple exclusion process (TASEP) with $N$ particles on a periodic lattice of $L$ sites is an interacting particle system with hopping rates breaking detailed balance. The total time-integrated current…
We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three…
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to…
A coarse-grained computational model is used to investigate the effect of a fluctuating fluid membrane on the dynamics of patchy-particle assembly into virus capsid-like cores. Results from simulations for a broad range of parameters are…
Computational modeling of high entropy alloys (HEA) is challenging given the scalability issues of Density functional theory (DFT) and the non-availability of Interatomic potentials (IP) for molecular dynamics simulations (MD). This work…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an…
We study the effects of thermal fluctuations on symmetric tensionless heterogeneous (two-component) fluid membranes in a simple minimal model. Close to the critical point $T_c$ of the associated miscibility phase transition of the…
We present the multicomponent functionalized free energies that characterize the low-energy packings of amphiphilic molecules within a membrane through a correspondence to connecting orbits within a reduced dynamical system. To each…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
We investigate the probability distribution of the quantum fluctuations of thermodynamic functions of finite, ballistic, phase-coherent Fermi gases. Depending on the chaotic or integrable nature of the underlying classical dynamics, on the…
From the events generated from the MC code of a multi-phase transport (AMPT) model with string melting, the properties of multiplicity fluctuations of charged particles in Pb-Pb collisions at $\sqrt{s_{\mathrm{NN}}}=\rm{~2.76 \,TeV}$ are…
The probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with $\exp(-\psi_N)$, where…