相关论文: A Rational Approach to Ring Flexibility in Interna…
The interplay of nematic order and phase separation in solutions of semiflexible polymers in solvents of variable quality is investigated by density functional theory (DFT) and molecular dynamics (MD) simulations. We studied coarse-grained…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
We consider a phantom chain model of polymer with internal friction in a harmonic confinement and extend it to take care of effects of solvent quality following a mean field approach where an exponent $\nu$ is introduced. The model termed…
The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolecular knots, such as knotted proteins, bear various cellular…
We investigated the static and dynamic properties of a Rouse ring polymer modified by introducing an effective, spherically symmetric, attractive potential of entropic nature and a memory function describing the effect of dynamic…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
Accurate frictional contact is critical in simulating the assembly of rod-like structures in the practical world, such as knots, hairs, flagella, and more. Due to their high geometric nonlinearity and elasticity, rod-on-rod contact remains…
Molecular dynamics (MD) employing machine-learned interatomic potentials (MLIPs) serve as an efficient, urgently needed complement to ab initio molecular dynamics (aiMD). By training these potentials on data generated from ab initio…
The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…
Contact dynamics (CD) is a powerful method to solve the dynamics of large systems of colliding rigid bodies. CD can be computationally more efficient than classical penalty-based discrete element methods (DEM) for simulating contact between…
The dynamic oxygen migration at the interface of carbon allotropes dominated by the periodic hexagonal rings, including graphene and carbon nanotube, has opened up a new avenue to realize dynamic covalent materials. However, for the carbon…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexibility of both proteins and ligands challenges conventional…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
In the perspective of developing smart hybrid materials with customized features, ferrogels and magnetorheological elastomers allow a synergy of elasticity and magnetism. The interplay between elastic and magnetic properties gives rise to a…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
Curvatures in the most probable rupture force ($f^*$) versus log-loading rate ($\log{r_f}$) observed in dynamic force spectroscopy (DFS) on biomolecular complexes are interpreted using a one-dimensional free energy profile with multiple…
This study presents a set of algorithms that deal with trajectory planning of rational single-loop mechanisms with one degree of freedom (DoF). Benefiting from a dual quaternion representation of a rational motion, a formula for direct…
In this thesis I generalize Ring Polymer Molecular Dynamics (RPMD) rate theory to electronically non-adiabatic systems, followed by application to two one-dimensional curve crossing models and a multidimensional spin-boson model.
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…