Related papers: Mesoscopic helical models for DNA
We use light-front Holography to estimate the valence quark and the meson cloud contributions to the nucleon axial form factor. The free couplings of the holographic model are determined by the empirical data and by the information…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
We present a Hamiltonian formulation for the linearized Vlasov-Maxwell system with a Maxwellian background distribution function. We discuss the geometric properties of the model at the continuous level, and how to discretize the model in…
This paper presents PANIC, a 3D discrete mesoscale dislocation dynamics model which includes a fully quantitative treatment of both dislocation climb and dislocation glide, including climb driven by both osmotic and mechanical stresses and…
Accurately predicting friction in sliding interfaces that contain third body wear particles is critical for engineering applications such as sliding movement in pistons, bearings, or metal forming. We present a hierarchical multiscale…
Elastic interactions arising from a difference of lattice spacing between two coherent phases can have a strong influence on the phase separation (coarsening) of alloys. If the elastic moduli are different in the two phases, the elastic…
A computational procedure that allows the detection of a new type of high-dimensional chaotic saddle in Hamiltonian systems with three degrees of freedom is presented. The chaotic saddle is associated with a so-called normally hyperbolic…
Recent advancements in the generation of mid-infrared and terahertz laser pulses have enabled us to observe strong-field driven non-perturbative high-harmonic generation (HHG) from semiconductors, dielectrics, and semimetals. HHG has added…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear, computationally intensive, and can be difficult to interpret, while often only…
In recent experiments involving PNIPAM copolymers it has been observed that stable spherical nanoparticles are being formed by association of several chains in poor aqueous solution instead of aggregation. This type of mesoscopic structures…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
Research on transport, self-assembly and defect dynamics within confined, flowing liquid crystals requires versatile and computationally efficient mesoscopic algorithms to account for fluctuating nematohydrodynamic interactions. We present…
We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response.…
Structure predictions of helical membrane proteins have been designed to take advantage of the structural autonomy of secondary structure elements, as postulated by the two-stage model of Engelman and Popot. In this context, we investigate…
Higher order closed-form formulation for Neo-Hookean shell is presented. New solution for natural frequency of free vibration of a hemisphere is derived.
Highly oriented solid-supported lipid membranes in stacks of controlled number $N \simeq 16$ (oligo-membranes) have been prepared by spin-coating using the uncharged lipid model system 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). The…
Machine Learning (ML) techniques are revolutionizing the way to perform efficient materials modeling. Nevertheless, not all the ML approaches allow for the understanding of microscopic mechanisms at play in different phenomena. To address…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…