Related papers: Protein Folding as a Quantum Transition Between Co…
All stem cell fate transitions, including the metabolic reprogramming of stem cells and the somatic reprogramming of fibroblasts into pluripotent stem cells, can be understood from a unified theoretical model of cell fates. Each cell fate…
Suppose a quantum system starts to evolve under a Hamiltonian from some initial state. When for the first time, will an observable attain a preassigned value? To answer this question, one method often adopted is to make instantaneous…
Nascent quantum computers motivate the exploration of quantum many-body systems in nontraditional scenarios. For example, it has become natural to explore the dynamics of systems evolving under both unitary evolution and measurement. Such…
Processes that proceed reliably from a variety of initial conditions to a unique final form, regardless of moderately changing conditions, are of obvious importance in biophysics. Protein folding is a case in point. We show that the action…
We investigate the time evolution of the thermopower in a vibrating quantum dot suddenly shifted into the Kondo regime via a gate voltage by adopting the time-dependent non-crossing approximation and linear response Onsager relations.…
A model of quantum measurement, illustrated using the spin--boson model, is formulated in terms of a cascading pair of quantum phase transitions. The first produces the desired superposition of macroscopic responses to the microscopic state…
The motion of a conducting electron in a quantum dot with one or several dislocations in the underlying crystal lattice is considered in the continuum picture, where dislocations are represented by torsion of space. The possible effects of…
This dissertation unifies one of the central methods of classical rate calculation, `Transition-State Theory' (TST), with quantum mechanics, thereby deriving a rigorous `Quantum Transition-State Theory' (QTST). The resulting QTST is…
Many of the concepts which are at the basis of the development associated with a quantitative treatment of the variety of phenomena associated with the spontaneous breaking of gauge symmetry in nuclei have been instrumental in connection…
This work presents the implementation of a fragment-based, quantum-centric supercomputing workflow for computing molecular electronic structure using quantum hardware. The workflow is applied to predict the relative energies of two…
Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…
We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS)…
The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective…
Modeling environments that are not in local thermal equilibrium, such as protoplanetary disks or planetary atmospheres, with molecular spectroscopic data from space telescopes requires knowledge of the rate coefficients of rovibrationally…
We investigate the inelastic spin-flip rate for electrons in a quantum dot due to their contact hyperfine interaction with lattice nuclei. In contrast to other works, we obtain a spin-phonon coupling term from this interaction by taking…
Accurate prediction of electron temperature ($T_{\rm e}$) is critical for non-equilibrium plasma applications ranging from hypersonic flight to plasma-assisted combustion. We recently proposed a thermodynamically consistent model for…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…
How long does it take to entangle two distant qubits in a quantum circuit evolved by generic unitary dynamics? We show that if the time evolution is followed by measurements of all but two infinitely separated test qubits, then the…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…