Related papers: The minimal molecular surface
Low energy supersymmetric models provide a solution to the hierarchy problem and also have the necessary ingredients to solve two of the most outstanding issues in cosmology: the origin of dark matter and baryonic matter. One of the most…
We present the marginal unbiased score expansion (MUSE) method, an algorithm for generic high-dimensional hierarchical Bayesian inference. MUSE performs approximate marginalization over arbitrary non-Gaussian latent parameter spaces,…
RNA structure determination is essential for understanding its biological functions. However, the reconstruction process often faces challenges, such as atomic clashes, which can lead to inaccurate models. To address these challenges, we…
Response Surface Methodology (RSM) introduced in the paper (Box & Wilson, 1951) explores the relationships between explanatory and response variables in complex settings and provides a framework to identify correct settings for the…
Several cellular activities, such as directed cell migration, are coordinated by an intricate network of biochemical reactions which lead to a polarised state of the cell, in which cellular symmetry is broken, causing the cell to have a…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Multidimensional scaling (MDS) is a popular dimensionality reduction techniques that has been widely used for network visualization and cooperative localization. However, the traditional stress minimization formulation of MDS necessitates…
Manifold learning (ML) aims to seek low-dimensional embedding from high-dimensional data. The problem is challenging on real-world datasets, especially with under-sampling data, and we find that previous methods perform poorly in this case.…
Differentiating signals from the background in micrographs is a critical initial step for cryogenic electron microscopy (cryo-EM), yet it remains laborious due to low signal-to-noise ratio (SNR), the presence of contaminants and densely…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
Simple wavefunctions of low computational cost but which can achieve qualitative accuracy across the whole potential energy surface (PES) are of relevance to many areas of electronic structure as well as to applications to dynamics. Here,…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
The study of biomolecular folding has been greatly advanced by single-molecule force spectroscopy (SMFS), which enables the observation of the dynamics of individual molecules. However, extracting quantitative models of fundamental…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
Direct numerical simulation (DNS) of turbulent reactive flows has been the subject of significant research interest for several decades. Accurate prediction of the effects of turbulence on the rate of reactant conversion, and the subsequent…
This paper reports on a novel template-free monocular non-rigid surface reconstruction approach. Existing techniques using motion and deformation cues rely on multiple prior assumptions, are often computationally expensive and do not…
We present a general construction of embedded minimal and constant mean curvature surfaces in $\mathbb{S}^n$ and one-phase free boundaries joined by a smooth interpolation by capillary hypersurfaces. This framework recovers all known…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
The minimal dominating Set (MDS) problem is a prototypical hard combinatorial optimization problem. Two years ago we studied this problem by cavity method. Although we get the solution of a given graph, which gives very good estimation of…