Related papers: Probing the Dark Energy in the Functional Protein …
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this…
We investigate the value of future dark energy experiments by modeling their ability to constrain the dark energy equation of state. Similar work was recently reported by the Dark Energy Task Force (DETF) using a two dimensional…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
Dynamical wave function collapse models entail the continuous liberation of a specified rate of energy arising from the interaction of a fluctuating scalar field with the matter wave function. We consider the wave function collapse process…
Cosmology enters precision testing period with the observational experiments advancement. We have not arrived to decipher the origin of the dominant dark energy component of our universe, although we have located some of its characters. In…
Dark energy and dark matter are only indirectly measured via their gravitational effects. It is possible that there is an exchange of energy within the dark sector, and this offers an interesting alternative approach to the coincidence…
The distribution of angles subtended between pairs of galaxies and the line of sight,which is uniform in real space, is distorted by their peculiar motions, and has been proposed as a probe of cosmic expansion. We test this idea using…
In this PhD thesis, we explore and apply methods inspired by the free energy principle to two important areas in machine learning and neuroscience. The free energy principle is a general mathematical theory of the necessary…
The use of machine learning to estimate the energy of a group of atoms, and the forces that drive them to more stable configurations, has revolutionized the fields of computational chemistry and materials discovery. In this domain, rigorous…
A significant observational effort has been directed to unveil the nature of the so-called dark energy. However, given the large number of theoretical possibilities, it is possible that such a task cannot be performed on the basis only of…
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the…
Protein conformational changes are activated processes essential for protein functions. Activation in a protein differs from activation in a small molecule in that it involves directed and systematic energy flows through preferred channels…
Partial localization is the phenomenon of self-aggregation of mass into high-density structures that are thin in one direction and extended in the others. We give a detailed study of an energy functional that arises in a simplified model…
The observed cosmic acceleration was attributed to an exotic dark energy in the framework of classical general relativity. The dark energy behaves very similar with vacuum energy in quantum mechanics. However, once the quantum effects are…
The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native…
A central challenge in the study of protein evolution is the identification of historic amino acid sequence changes responsible for creating novel functions observed in present-day proteins. To address this problem, we developed a new…
We investigate cosmological models in which dynamical dark energy consists of a scalar field whose present-day value is controlled by a coupling to the neutrino sector. The behaviour of the scalar field depends on three functions: a kinetic…
We study the dynamical properties and space distribution of dark energy in the weak and strong gravitational fields caused by inhomogeneities of matter in the static world of galaxies and clusters. We show that the dark energy in the weak…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…