Related papers: Self Consistent Field Theory of Virus Assembly
Understanding the asymptotic behavior of reaction-diffusion (RD) systems is crucial for modeling processes ranging from species coexistence in ecology to biochemical interactions within cells. In this work, we analyze RD systems in which…
The Kohn-Sham gaps of density functional theory (DFT) obtained in terms of local density approximation (LDA) or generalized gradient approximation (GGA) cannot be directly linked to the fundamental gaps of semiconductors, but in engineering…
Many spherical viruses encapsulate their genome in protein shells with icosahedral symmetry. This process is spontaneous and driven by electrostatic interactions between positive domains on the virus coat proteins and the negative genome.…
We extend the recently proposed thermally-assisted-occupation density functional theory (TAO-DFT) [J.-D. Chai, J. Chem. Phys. 136, 154104 (2012)] to generalized-gradient approximation (GGA) exchange-correlation density functionals. Relative…
A complete understanding of a material requires both knowledge of the excited states as well as of the ground state. In particular, the low energy excitations are of utmost importance while studying the electronic, magnetic, dynamical, and…
In a previous article [E.M. Blokhuis, K.I. Skau, and J.B. Avalos, J. Chem. Phys. 119, 3483 (2003)], a self-consistent field formalism was derived for weakly adsorbing polymers, valid for any chain length. It was shown that the presence of a…
The self-consistent Thomas-Fermi approximation is an essential method for studying the non-uniform nuclear matter with relativistic mean-field theory. In this method, the nucleon distribution in the Wigner-Seitz cell is obtained…
The self-consistent mean-field (SCMF) theory describes many properties of the ground state and excited states of the atomic nucleus, such as masses, radii, deformations and giant resonance energies. SCMF models are based on the independent…
Kohn-Sham density functional theory (DFT) has long struggled with the accurate description of strongly correlated and open shell systems and improvements have been minor even in the newest hybrid functionals. In this Letter we treat the…
Effective field theory (EFT) methods are applied to density functional theory (DFT) as part of a program to systematically go beyond mean-field approaches to medium and heavy nuclei. A system of fermions with short-range, natural…
The electronic structure of the zero-gap two-dimensional graphene has a charge neutrality point exactly at the Fermi level that limits the practical application of this material. There are several ways to modify the Fermi-level-region of…
Most applications of time-dependent density-functional theory (TDDFT) use the adiabatic local-density approximation (ALDA) for the dynamical exchange-correlation potential Vxc(r,t). An exact (i.e., nonadiabatic) extension of the…
Understanding how virus capsids assemble around their nucleic acid (NA) genomes could promote efforts to block viral propagation or to reengineer capsids for gene therapy applications. We develop a coarse-grained model of capsid proteins…
Standard approximations for the exchange-correlation (XC) functional in Kohn-Sham density functional theory (KS-DFT) typically lead to unacceptably large errors when applied to strongly-correlated electronic systems. Partition-DFT (PDFT) is…
We derive the self-consistent random phase approximations (sc-RPA) from the projective truncation approximation (PTA) for the equation of motion of two-time Green's function. The obtained sc-RPA applies to arbitrary temperature and recovers…
We demonstrate in the present study that self-consistent calculations based on the self-energy functional theory (SFT) are possible for the electronic structure of realistic systems in the context of quantum chemistry. We describe the…
RNA viruses are known to replicate with extremely high mutation rates. These rates are actually close to the so-called error threshold. This threshold is in fact a critical point beyond which genetic information is lost through a…
Site density functional theory (SDFT) provides a rigorous framework for statistical mechanics analysis of inhomogeneous molecular liquids. The key defining feature of these systems is the presence of two very distinct interactions scales…
The single-cell RNA sequencing (scRNA-seq) technology enables researchers to study complex biological systems and diseases with high resolution. The central challenge is synthesizing enough scRNA-seq samples; insufficient samples can impede…
Single-cell RNA sequencing (scRNA-seq) provides high-dimensional profiles of cellular states, enabling data-driven modeling of cellular dynamics over time. In practice, time-resolved scRNA-seq is collected at only a few discrete time points…