Related papers: Protein conformational dynamics and electronic str…
Quantum coherence is highly involved in photochemical functioning of complex molecular systems. Co-existence and intermixing of electronic and/or vibrational coherences, while never unambiguously identified experimentally, has been proposed…
We explore the possibility that the reported time variation of the fine structure constant $\alpha$ is due to a coupling between electromagnetism and gravitation. This may reconcile the claimed results on $\alpha$ with the upper limit from…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
We present an improved approach for generating a set of optimized frontier orbitals (HOMO and LUMO) that minimizes the energy of one double configuration. We further benchmark the effect of including such a double within a CIS or TD-DFT…
We study a large data set of protein structure ensembles of very diverse sizes determined by nuclear magnetic resonance. By examining the distance-dependent correlations in the displacement of residues pairs and conducting finite size…
We discuss a method to calculate with quantum molecular dynamics simulations the rate of energy exchanges between electrons and ions in two-temperature plasmas, liquid metals and hot solids. Promising results from this method were recently…
A new statistical mechanics formulation of characterizing the structural fluctuation of protein correlated with that of water is presented based on the generalized Langevin equation and the 3D-RISM/RISM theory of molecular liquids. The…
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
In the crowded eukaryotic nucleus, euchromatin and heterochromatin segregate into distinct compartments, a phenomenon often attributed to homotypic interactions mediated by liquid liquid phase separation of chromatin associated proteins.…
Using Bayesian inference, we determine probabilistic constraints on the parameters describing the fluctuating structure of protons at high energy. We employ the color glass condensate framework supplemented with a model for the spatial…
We consider the scenario of a fluctuating spacetime due to a deformed commutation relation with a fluctuating deformation parameter, or to a fluctuating metric tensor. By computing the resulting dynamics and averaging over these…
An ab-initio method for determining the dynamical structure function of an interacting many--body quantum system has been devised by combining a generalized integral transform method with Quantum Monte Carlo methods. As a first application,…
The theory of mesoscopic fluctuations is applied to inhomogeneous solids consisting of chaotically distributed regions with different crystalline structure. This approach makes it possible to describe statistical properties of such mixture…
In this article, we explore the dynamical decoherence of the chromophores within a green fluorescent protein when coupled to a finite-temperature dielectric environment. Such systems are of significant interest due to their anomalously long…
The coherent dynamics of vibronic wave packets in the green fluorescent protein is reported. At room temperature the non-stationary dynamics following impulsive photoexcitation displays an oscillating optical transmissivity pattern with…
Discontinuous changes in the electronic structure upon infinitesimal changes to the Hamiltonian are demonstrated. Remarkably, these are revealed in one and two electron molecular systems if the realm of the nuclear charge is extended to be…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
Electronic decoherence processes in trans-polyacetylene oligomers are considered by explicitly computing the time dependent molecular polarization from the coupled dynamics of electronic and vibrational degrees of freedom in a mean-field…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances…