Related papers: A Coarse-Grained Model for Predicting RNA Folding …
For multilayer structures, interfacial failure is one of the most important elements related to device reliability. For cohesive zone modelling, traction-separation relations represent the adhesive interactions across interfaces. However,…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…
The temperature dependence of mechanical properties of steel nanowires with varying carbon content was studied using molecular dynamics simulations. Four interatomic potentials were assessed, with the Modified Embedded Atom Method (MEAM)…
We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand…
Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
We develop a coarse-grained protein model with a simplified amino acid interaction potential. We perform discrete molecular dynamics folding simulations of a small 20 residue protein - Trp-cage - from a fully extended conformation. We…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
We calculate the thermophoretic drift of a charged single colloidal particle with hydrodynamically slipping surface immersed in an electrolyte solution in response to a small temperature gradient. Here, we rely on a linearized hydrodynamic…
The complexity of biomolecular interactions necessitates advanced methodologies to accurately capture their behavior in solution. In this work, we focus on monoclonal antibodies and adopt a multi-scale coarse-graining strategy for their…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
RNA folding prediction remains challenging, but can be also studied using a topological mathematical approach. In the present paper, the mathematical method to compute the topological classification of RNA structures and based on matrix…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
Computer simulations can provide mechanistic insight into ionic liquids (ILs) and predict the properties of experimentally unrealized ion combinations. However, ILs suffer from a particularly large disparity in the time scales of atomistic…
We derive a Debye-H\"uckel-like model of the electric ion-ion interaction for non-constant dielectric susceptibility, which does not depend on any kind of charging process due to its foundation in the general framework of non-equilibrium…
Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of…
We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore,…
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
Recent progress has been made in the numerical modelling of neutral microgel particles with a realistic, disordered structure. In this work we extend this approach to the case of co-polymerised microgels where a thermoresponsive polymer is…