Related papers: Analysis of Two-State Folding Using Parabolic Appr…
Recent studies attracted the attention on the inherent structure landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single…
We review the leading momentum, frequency and temperature dependences of the single particle self-energy and the corresponding term in the entropy of a two dimensional Fermi liquid (FL) with a free particle spectrum. We calculate the…
A self-consistent thermodynamic model of metallic system is presented. The expression for the Gibbs energy is derived, which incorporates elastic (static) energy, vibrational energy within the Debye model, and electronic part in Hartee-Fock…
We consider the entropy production of a strongly coupled bipartite system. The total entropy production can be partitioned into various components, which we use to define local versions of the Second Law that are valid without the usual…
The thermodynamics with medium effects expressed by the dispersion relation of the temperature and density dependent particle mass is studied. Many previous treatments have been reviewed. A new thermodynamical treatment based on the…
Gibbs states are a natural model of quantum matter at thermal equilibrium. We investigate the role of external fields in shaping the entanglement structure and computational complexity of high-temperature Gibbs states. External fields can…
The Gibbs distribution universally characterizes states of thermal equilibrium. In order to extend the Gibbs distribution to non-equilibrium steady states, one must relate the self-information $\mathcal{I}(x) = -\log(P_\text{ss}(x))$ of…
We study the dynamics of two interacting two-level systems (qubits) having one of them isolated and the other coupled to a single mode electromagnetic field in a thermal state. The field plays the role of a small environment, in contrast to…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
The invariant mass of free particles is used to derive a bound-state equation for the hydrogen atom at rest. This equation has the well-known solutions for the single-particle states. Existence of two-particle bound states, for which the…
The present paper studies a large class of temperature dependent probability distributions and shows that entropy and energy can be defined in such a way that these probability distributions are the equilibrium states of a generalized…
We demonstrate a new method to directly manipulate the state of individual two-level systems (TLS) in phase qubits. It allows one to characterize the coherence properties of TLS using standard microwave pulse sequences, while the qubit is…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
We examine temperature dependent picosecond dynamics as a function of structure and function for lysozyme and cytochrome c using temperature dependent terahertz permittivity measurements. A double Arrhenius temperature dependence with…
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…
In cellular environment, confinement and macromulecular crowding play an important role on thermal stability and folding kinetics of a protein. We have resorted to a generalized version of the Wako-Saito-Munoz-Eaton model for protein…
As a prototype of systems bearing a localization-delocalization transition, the strand-separation (melting) process in a double-stranded biopolymer is studied by a mapping to a quantum-mechanical problem with short-ranged potentials. Both…
A continuum plasticity model for metals is presented from considerations of non-equilibrium thermodynamics. Of specific interest is the application of a fluctuation relation that subsumes the second law of thermodynamics en route to…
Using a generalized Bohr model and the hyper-spherical formalism for a three-body system, we derive the Thomas theorem assuming a simple interaction depending on the range of the potential. We discuss the conditions for which an unbound…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…