Related papers: Off-lattice simulation of the solid phase DNA ampl…
The impact of damping effect and external forces to the DNA breathing is investigated within the Peyrard-Bishop model. In in the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger…
An extension of the Random Sequential Adsorption (RSA) model has been proposed recently, motivated by the coverage of oil droplets by DNA-functionalized colloidal particles. Particles arrive to a flat substrate with a uniform flux F but…
A function $f: \mathbb{R}^d \rightarrow \mathbb{R}$ is referred to as a Sparse Additive Model (SPAM), if it is of the form $f(\mathbf{x}) = \sum_{l \in \mathcal{S}}\phi_{l}(x_l)$, where $\mathcal{S} \subset [d]$, $|\mathcal{S}| \ll d$.…
The dynamics of compaction of hard cross-shaped pentamers on the 2D square lattice is investigated. The addition of new particles is controlled by diffusive relaxation. It is shown that the filling process terminates at a glassy phase with…
A numerical study of the statistics of transmission ($t$) and reflection ($r$) of quasi-particles from a one-dimensional disordered lasing or amplifying medium is presented. The amplification is introduced via a uniform imaginary part in…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Efficient capture and detection of minute amount of deoxyribonucleic acid (DNA) molecules are pivotal for an array of modern gene technologies which are widely utilized in medical, forensic and defense applications, including DNA…
A particularly simple setup is introduced to study the influence of time-delayed coherent feedback on the optical squeezing properties of the degenerate parametric amplifier (DPA). The possibility for significantly enhanced squeezing is…
We analyze the properties of a class of improved lattice topological charge density operators, constructed by a smearing-like procedure. By optimizing the choice of the parameters introduced in their definition, we find operators having (i)…
Subsampling layers play a crucial role in deep nets by discarding a portion of an activation map to reduce its spatial dimensions. This encourages the deep net to learn higher-level representations. Contrary to this motivation, we…
We studied the excitation process of silicon under an intense double pulse. We employed the three-temperature (electron, hole, and lattice) model (3TM) together with Maxwell's equations. We solved Maxwell's equations by the…
We introduce a new method for simulating photoemission spectra from bulk crystals in the ultra-violet energy range, within a three-step model. Our method explicitly accounts for transmission and matrix-element effects, as calculated from…
We study diffusion of hardcore particles on a one dimensional periodic lattice subjected to a constraint that the separation between any two consecutive particles does not increase beyond a fixed value $(n+1);$ initial separation larger…
We study the ground-state properties of spin-1/2 fermionic atoms confined in a one-dimensional optical superlattice with harmonic confinement by using the density matrix renormalization group method. For this purpose, we consider an ionic…
Augmentation is an effective alternative to utilize the small amount of labeled protein data. However, most of the existing work focuses on design-ing new architectures or pre-training tasks, and relatively little work has studied data…
Here, we propose a platform based on ultra-cold fermionic molecules trapped in optical lattices to simulate nonadiabatic effects, as they appear in certain molecular dynamical problems. The idea consists of a judicious choice of two…
The formation and dissociation of bosonic molecules in an optical lattice, formed by spin-1/2 fermionic atoms, is considered in the presence of an attractive nearest-neighbor interaction. A mean-field approximation reveals three different…
We introduce a lattice fermion-Higgs model with one component `reduced staggered' fermions. In order to use the fermion field as efficiently as possible we couple the two {\em staggered} flavors to the O(4) Higgs field leading to a model…
Due to particle conservation, Canonical Molecular Dynamics (MD) simulations fail in the description of surface phase transitions involving coverage or lateral density changes. However, a step on the surface can act effectively as a source…
Off-policy evaluation (OPE) is one of the most fundamental problems in reinforcement learning (RL) to estimate the expected long-term payoff of a given target policy with only experiences from another behavior policy that is potentially…