Related papers: Off-lattice simulation of the solid phase DNA ampl…
The O(n) non-linear $\sigma$-model is simulated on 2-dimensional regular and random lattices. We use two different levels of randomness in the construction of the random lattices and give a detailed explanation of the geometry of such…
We describe a simple model of fermions in quasi-one dimension that features interaction induced deconfinement (a phase transition where the effective dimensionality of the system increases as interactions are turned on) and which can be…
Thermalcycler were extensively used machine for amplify DNA sample. One of the major problems in the working time was that it spent most of time for cooling and heating. In order to improve the efficient, this study presented a novel method…
A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But,…
Self-avoidance is a common mechanism to improve the efficiency of a random walker for covering a spatial domain. However, how this efficiency decreases when self-avoidance is impaired or limited by other processes has remained largely…
Low latency models are critical for real-time speech enhancement applications, such as hearing aids and hearables. However, the sub-millisecond latency space for resource-constrained hearables remains underexplored. We demonstrate speech…
Fermionic atoms in a periodic optical lattice provide a realization of the single-band Hubbard model. Using Quantum Monte Carlo simulations along with the Maximum Entropy Method, we evaluate the effect of a time-dependent perturbative…
We extend the lipid-structured model for atherosclerotic plaque development of Ford et al. (2019) to account for macrophage proliferation. Proliferation is modelled as a non-local decrease in the lipid structural variable that is similar to…
Molecular dynamics (MD) simulation is widely used to study protein conformations and dynamics. However, conventional simulation suffers from being trapped in some local energy minima that are hard to escape. Thus, most computational time is…
Unravelling competing orders emergent in doped Mott insulators and their interplay with unconventional superconductivity is one of the major challenges in condensed matter physics. To explore possible superconductivity state in the doped…
We present a detailed kinetic model for the Polymerase Chain Reaction, and model the probability of replication in terms of the physical parameters of the problem. Applying the theory of branching processes, we show the existance of a new…
We present a computationally efficient general first-principles based method for spin-lattice simulations for solids. Our method is based on a combination of atomistic spin dynamics and molecular dynamics, expressed through a spin-lattice…
A function $f: \mathbb{R}^d \rightarrow \mathbb{R}$ is a Sparse Additive Model (SPAM), if it is of the form $f(\mathbf{x}) = \sum_{l \in \mathcal{S}}\phi_{l}(x_l)$ where $\mathcal{S} \subset [d]$, $|\mathcal{S}| \ll d$. Assuming $\phi$'s,…
The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated…
Under appropriate conditions, mixtures of cationic and neutral lipids and DNA in water condense into complexes in which DNA strands form local 2D smectic lattices intercalated between lipid bilayer membranes in a lamellar stack. These…
Spike propagation for spatially correlated inputs in layered neural networks has been investigated with the use of a semi-analytical dynamical mean-field approximation (DMA) theory recently proposed by the author [H. Hasegawa, Phys. Rev. E…
The adsorption of atomic oxygen and its inclusion into subsurface sites on Ag(210) and Ag(410) surfaces have been investigated using density functional theory. We find that--in the absence of adatoms on the first metal layer--subsurface…
Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting…
Based on the so called $t$-$\phi$ model in two-dimensional (2D) lattices, we investigate the stabilities of a class of extended staggered-flux (SF) phases (which are the extensions of the $\sqrt{2}\times\sqrt{2}$ SF phase to generalized…
Compression of an intense laser pulse using backward Raman amplification (BRA) in plasma, followed by vacuum focusing to a small spot size, can produce unprecedented ultrarelativistic laser intensities. The plasma density inhomogeneity…