Related papers: Visualization and thermodynamic encoding of single…
The standard variational derivation of stellar matter structure in the Wigner-Seitz approximation is generalized to the finite temperature situation where a wide distribution of different nuclear species can coexist in the same density and…
We have analyzed with pedagogical purposes the relation of the total densities of states (TDOS/PDOS/OPDOS) and molecular orbital diagrams (MOD) for single and isolated molecules of Water and Nitrogen. We use a calculation level HF/6-311G,…
For classical discrete systems under constant composition, a set of microscopic state dominantly contributing to thermodynamically equilibrium structure should depend on temperature and energy through Boltzmann factor, exp(-bE). Despite…
First-principles molecular dynamics simulation based on a plane wave/pseudopotential implementation of density functional theory is adopted to investigate atomic scale energy transport for semiconductors (silicon and germanium). By imposing…
Machine-learning methods in biochemistry commonly represent molecules as graphs of pairwise intermolecular interactions for property and structure predictions. Most methods operate on a single graph, typically the minimal free energy (MFE)…
A modeling framework for the internal conformational dynamics and external mechanical movement of single biological macromolecules in aqueous solution at constant temperature is developed. Both the internal dynamics and external movement…
Quantum mechanical phenomena, such as electronic coherence and entanglement, play a key role in achieving the unrivalled efficiencies of light-energy conversion in natural photosynthetic light-harvesting complexes, and triggered the growing…
We prove that the transport of any differentiable scalar observable in $d$-dimensional non-equilibrium systems is bounded from above by the total entropy production scaled by the amount the observation "stretches" microscopic coordinates.…
Using a simple example of biological macromolecules which are partitioned between bulk solution and membrane, we investigate T.L. Hill's phenomenological nanothermodynamics for small systems. By introducing a {\em systems size dependent}…
Simulations are performed of a small quantum system interacting with a quantum environment. The system consists of various initial states of two harmonic oscillators coupled to give normal modes. The environment is "designed" by its level…
An atomistic approach is used to investigate finite-temperature properties of ferroelectric nanodots that are embedded in a polarizable medium. Different phases are predicted, depending on the ferroelectric strengths of the material…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
We derive an exact recursion formula for the calculation of thermodynamic functions of finite systems obeying Bose-Einstein statistics. The formula is applicable for canonical systems where the particles can be treated as noninteracting in…
Classical-like formulas are given in order to evaluate thermal averages of observables belonging to a quantum nonlinear system with dissipation described by the Caldeira-Leggett model [Phys. Rev. Lett. 46, 211 (1981); Ann. Phys. (N.Y.) 149,…
Absorption microscopy is a powerful technique, enabling the detection of single non- fluorescent molecules at room temperature. So far, the molecular absorption has been probed optically via the attenuation of a probing laser. The…
A novel geometric formalism for statistical estimation is applied here to the canonical distribution of classical statistical mechanics. In this scheme thermodynamic states, or equivalently, statistical mechanical states, can be…
Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level…
We demonstrate complete control over dynamics of a single superconducting vortex in a nanostructure which we coin the Single Vortex Box (SVB). Our device allows us to trap the vortex in a field-cooled aluminum nanosquare and expel it on…
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form…