Related papers: Statistical Mechanics of Integral Membrane Protein…
This paper investigates the asymptotic behavior of the Helmholtz free energy of mixtures at small compressibility. We start from a general representation for the local free energy that is valid in stable subregions of the phase diagram. On…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
We consider stochastic energy balance and entropy production (EP) in a generalized Langevin dynamics of macrospins, allowing for both amplitude and direction fluctuations, under external magnetic field. EP is calculated using Fokker-Planck…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We provide a complete thermodynamic solution of a 1D hopping model in the presence of a random potential by obtaining the density of states. Since the partition function is related to the density of states by a Laplace transform, the…
The antisymmetrized molecular dynamics (AMD) simulations suggest that the isospin composition of fragments produced dynamically in multifragmentation reactions is basically governed by the symmetry energy of low-density uniform nuclear…
We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wildtype structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…
We study the distribution of the minimum free energy (MFE) for the Turner model of pseudoknot free RNA secondary structures over ensembles of random RNA sequences. In particular, we are interested in those rare and intermediate events of…
In this paper, we discuss critical aspects of the mechanisms and features of polymer proton exchange membrane (PEM) degradation in low-temperature H2/O2 fuel cell. In this paper, we focused on chemical mechanism of OH radical generation and…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
We study Derrida's generalized random energy model in the presence of uniform external field. We compute the fluctuations of the ground state and of the partition function in the thermodynamic limit for all admissible values of parameters.…
Multiplicity distributions of intermediate mass fragments (IMF) seen in intermediate energy heavy ion collisions have been of great interest in the last ten years. The distributions of single intermediate sized element are close to…
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also…
The experimental emission probabilities of complex fragments by low energy compound nuclei and their dependence upon energy and atomic number are compared to the transition state rates. Intermediate-mass-fragment multiplicity distributions…
Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with $\exp(4N_e m(1 - 1/(2N)))$, where $m$ is Malthusian fitness and $N_e$ and…
Torsional-space Monte Carlo simulations of flexible molecules are usually based on the assumption that all values of dihedral angles have equal probability in the absence of atomic interactions. In the present paper it is shown that this…
Describing non-equilibrium properties of quantum many-body systems is challenging due to high entanglement in the wavefunction. We describe evolution of local observables via the influence matrix (IM), which encodes the effects of a…
The stability of a flexible fluid membrane containing a distribution of mobile, active proteins (e.g. proton pumps) is shown to depend on the structure and functional asymmetry of the proteins. A stable active membrane is in a…