Related papers: Analysis of Two-State Folding Using Parabolic Appr…
The second law of thermodynamics places a limitation into which states a system can evolve into. For systems in contact with a heat bath, it can be combined with the law of energy conservation, and it says that a system can only evolve into…
We solve a two dimensional model for polymer chain folding in the presence of mechanical pulling force ($f$) exactly using equilibrium statistical mechanics. Using analytically derived expression for the partition function we determine the…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
In the framework of open quantum systems, we study the internal dynamics of both freely falling and static two-level atoms interacting with quantized conformally coupled massless scalar field in de Sitter spacetime. We find that the atomic…
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…
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective…
The inhomogeneous cooling state describing the hydrodynamic behavior of a freely evolving granular gas strongly confined between two parallel plates is studied, using a Boltzmann kinetic equation derived recently. By extending the idea of…
We show how many-body ground state entanglement information may be extracted from sub-system energy measurements at zero temperature. A precise relation between entanglement and energy fluctuations is demonstrated in the weak coupling…
The potential energy problem in an electrostatically bound two-body system is studied in the framework of a recently proposed impact model of the electrostatic force and in analogy to the potential energy in a gravitationally bound system.…
Laboratory plasma production almost always preferentially heats either the ions or electrons, leading to a two-temperature state. High-fidelity modeling of these systems can be achieved with density functional theory molecular dynamics in…
We consider a Brownian particle in harmonic confinement of stiffness $k$, in one dimension in the underdamped regime. The whole setup is immersed in a heat bath at temperature $T$. The center of harmonic trap is dragged under any arbitrary…
In the framework of the theory of open systems based on completely positive quantum dynamical semigroups, we give a description of the continuous-variable entanglement for a system consisting of two noninteracting modes embedded in a…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
We investigate the influence of nearby two-level systems on the dynamics of a qubit. The intrinsic decoherence is given by a coupling of both the qubit and the two-level systems to a heat bath. Assuming weak interactions between the qubit…
Recently a number of approaches has been developed to connect the microscopic dynamics of particle systems to the macroscopic properties of systems in nonequilibrium stationary states, via the theory of dynamical systems. This way a direct…
A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of "macrostates" (e.g. sets of "microstates"), the consequence on…
We have presented a set of laws of entanglement thermodynamics for $T\bar{T}$-deformed CFTs and in general for $T^2$-deformed field theories. In particular, the first law of this set, states that although we are dealing with a non-trivial…
We investigate the time evolution of entanglement for bipartite systems of arbitrary dimensions under the influence of decoherence. For qubits, we determine the precise entanglement decay rates under different system-environment couplings,…
We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…