Related papers: Folding thermodynamics of model four-strand antipa…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
An important process for antimatter experiments is the cooling of particles in a Penning-Malmberg trap to experimentally useful temperatures. A non-neutral plasma of one species (e.g. antiprotons) can be collisionally cooled on another…
A hallmark of a thermodynamic phase transition is the qualitative change of system thermodynamic properties such as energy and heat capacity. On the other hand, no phase transition is thought to operate in the supercritical state of matter…
At ambient pressure CaFe2As2 has been found to undergo a first order phase transition from a high temperature, tetragonal phase to a low temperature orthorhombic / antiferromagnetic phase upon cooling through T ~ 170 K. With the application…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
We study the transition probabilities of a two-point measurement on a quantum system, initially prepared in a thermal state. We find two independent constraints on the difference between transition probabilities when the system is prepared…
We use gauge/gravity duality to study the thermodynamics of a generic almost conformal theory, specified by its beta function. Three different phases are identified, a high temperature phase of massless partons, an intermediate…
We study pressurised self-avoiding ring polymers in two dimensions using Monte Carlo simulations, scaling arguments and Flory-type theories, through models which generalise the model of Leibler, Singh and Fisher [Phys. Rev. Lett. Vol. 59,…
Motivated by experiments on doped transition metal oxides, this paper considers the interplay of interactions, disorder, kinetic energy and temperature in a simple system. An ensemble of two-site Anderson-Hubbard model systems has already…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
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 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…
We consider a one-dimensional gas of positive and negative unit charges interacting via a logarithmic potential, which is in thermal equilibrium at the (dimensionless) inverse temperature $\beta$. In a previous paper [Samaj, L.: J. Stat.…
We study the thermodynamics of clean, layered superconductor/ferromagnet nanostructures using fully self consistent methods to solve the microscopic Bogoliubov-deGennes equations. From these self-consistent solutions the condensation free…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
Many small proteins fold via a first-order "all-or-none" transition directly from an expanded coil to a compact native state. Here we study an analogous direct freezing transition from an expanded coil to a compact crystallite for a simple…