Related papers: Exact Statistical Mechanical Investigation of a Fi…
We consider a general lattice model of a finite protein in its environment and calculate its Boltzmann entropy SB(E) as a function of its energy E in a microcanonical ensemble, and Gibbs entropy SG(E) as a function of its average energy E…
In contrast to the canonical ensemble where thermodynamic functions are smooth for all finite system sizes, the microcanonical entropy can show nonanalytic points also for finite systems, even if the Hamiltonian is smooth. The relation…
We exploit a prescription to observe directly the physical properties of the thermodynamic limit under continuously applied field in one-dimensional quantum finite lattice systems. By systematically scaling down the energy of the…
The development of reliable methods for estimating microcanonical averages constitutes an important issue in statistical mechanics. One possibility consists of calculating a given microcanonical quantity by means of typical relations in the…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
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…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
We investigate a one-dimensional water-like lattice model with Van der Waals and hydrogen-bond interactions, allowing for particle number fluctuations through a chemical potential. The model, defined on a chain with periodic boundary…
In statistical physics, the challenging combinatorial enumeration of the configurations of a system subject to hard constraints (microcanonical ensemble) is mapped to a mathematically easier calculation where the constraints are softened…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…
A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable.…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
Here we investigate how local properties of particles in a thermal bath influence the thermodynamics of the bath. We utilize nanothermodynamics, based on two postulates: that small systems can be treated self-consistently by coupling to an…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
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…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
In this study, internal energy (U), electric field (E) and particle number (N) which specify the system quantities i.e. thermodynamical quantities for the proteins. In the frame of thermodynamical formalism, the relation between the heat…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…