Related papers: Self Consistent Field Theory of Virus Assembly
In cond-mat/9907125 the low-temperature behavior of a model for RNA secondary structure was studied. It is claimed that the model exhibits a breaking of the replica symmetry, since the width of the distribution P(q) of overlaps may converge…
To calculate static response properties of a many body system, local density approximation (LDA) can be safely applied. But applicability of LDA is limited for the case of dynamical response functions since dynamics of the system needs to…
Single molecule force spectroscopy of DNA strands adsorbed at surfaces is a powerful technique used in air or liquid environments to quantify their mechanical properties. Although the force responses are limited to unfolding events so far,…
We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and…
In the framework of the planar t-J model for cuprates we analyze the development of a pseudo gap in the density of states, which at low doping starts to emerge for temperatures T<J and persists up to the optimum doping. The analysis is…
Stochastic approximation (SA) and stochastic gradient descent (SGD) algorithms are work-horses for modern machine learning algorithms. Their constant stepsize variants are preferred in practice due to fast convergence behavior. However,…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
Diblock copolymers blended with homopolymer may self-assemble into spherical, cylindrical or lamellar aggregates. Transitions between these structures may be driven by varying the homopolymer molecular weight or the molecular weight or…
We study solvable spin chains, one-dimensional massless Dirac fermions, and conformal field theories (CFTs) with sine-square deformation (SSD), in which the Hamiltonian density is modulated by the function $f(x)=\sin^2 (\pi x/\ell)$, where…
We review the role of self-consistency in density functional theory. We apply a recent analysis to both Kohn-Sham and orbital-free DFT, as well as to Partition-DFT, which generalizes all aspects of standard DFT. In each case, the analysis…
We present an ab initio, self consistent density functional theory (DFT) description of ground state electronic and related properties of hexagonal boron nitride (hex-BN). We used a local density approximation (LDA) potential and the linear…
We report a detailed and systematic study of wave propagation through a stochastic absorbing random medium. Stochastic absorption is modeled by introducing an attenuation constant per unit length $\alpha$ in the free propagation region of…
During the lifecycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively…
Linear scaling density functional theory approaches to electronic structure are often based on the tendency of electrons to localize even in large atomic and molecular systems. However, in many cases of actual interest, for example in…
The random phase approximation (RPA) has received a considerable interest in the field of modeling systems where noncovalent interactions are important. Its advantages over widely used density functional theory (DFT) approximations are the…
Counterion adsorption on a flexible polyelectrolyte chain in a spherical cavity is considered by taking a "permuted" charge distribution on the chain so that the "adsorbed" counterions are allowed to move along the backbone. We compute the…
Unsupervised domain adaptation (UDA) has achieved unprecedented success in improving the cross-domain robustness of object detection models. However, existing UDA methods largely ignore the instantaneous data distribution during model…
A major challenge in using spin-flip time-dependent density functional theory (SF-TD-DFT) for spin-flip-down excitations is the presence of spin contamination. While several improved methods have been developed in the past, a simple and…
RNA velocity is an important model that combines cellular spliced and unspliced RNA counts to infer dynamical properties of various regulatory functions. Despite its wide applicability and many variants used in practice, the model has not…
The scaling of entanglement entropy with subsystem size fails to distinguish between gapped and gapless ground state of a scalar field theory in $d>1$ dimensions. We show that the scaling of angular momentum resolved entanglement entropy…