Related papers: Multiscale modelling of bionano interface
The potential of mean force (PMF) between two nano crystals (NCs) represents an effective interaction potential that can be used to study the assembly of NCs to various superstructures. For a given temperature, the effective interaction is…
We introduce the Hierarchically Interacting Particle Neural Network (HIP-NN) to model molecular properties from datasets of quantum calculations. Inspired by a many-body expansion, HIP-NN decomposes properties, such as energy, as a sum over…
A strategy is developed for generating equilibrated high molecular-weight polymer melts described with microscopic detail by sequentially backmapping coarse-grained (CG) configurations. The microscopic test model is generic but retains…
In this work, the blood NIR absorbances are recorded using the FT-IR method. It is shown that when the absorbance curves are multiplied by the first derivative of the water absorbance spectrum as well as by the first derivative of the…
Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…
Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting…
For the past decade, droplet interface bilayers (DIBs) have had an increased prevalence in biomolecular and biophysical literature. However, much of the underlying physics of these platforms are poorly characterized. To further the…
Protein-ligand interactions (PLIs) are fundamental to biochemical research and their identification is crucial for estimating biophysical and biochemical properties for rational therapeutic design. Currently, experimental characterization…
We propose unified data structures and algorithms for free-surface fluid simulations based on partial optimal transport, such as the Power Particles method or Gallou\"et-M\'erigot's scheme. Such methods previously relied on a discretization…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the…
This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…
In the last few decades, the development of miniature biological sensors that can detect and measure different phenomena at the nanoscale has led to transformative disease diagnosis and treatment techniques. Among others, biofunctional…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
Selective sensing of chiral molecules is a key aspect in fields spanning biology, chemistry, and pharmacology. However, conventional optical methods, such as circular dichroism (CD), encounter limitations owing to weak chiral light-matter…
We study the interaction of lipid bilayers with short chain alcohols using molecular dynamics on different length scales. We use detailed atomistic modeling and modeling on the length scale where an alcohol is just an amphiphilic dimer. Our…
Molecular dynamics simulation is employed to understand the thermodynamic behavior of cuboctahedron (cub) and icosahedron (ico) nanoparticles with 2-20 number of shells (55-28741 atoms). The embedded atom method was used to describe the…
Protein-surface interactions are ubiquitous in biological processes and bioengineering, yet are not fully understood. In biosensors, a key factor determining the sensitivity and thus the performance of the device is the orientation of the…
We investigated the translation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium…
We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian…